pax_global_header 0000666 0000000 0000000 00000000064 14060620177 0014515 g ustar 00root root 0000000 0000000 52 comment=0dccfae61b75759d224dc72f18b01cca1c063c23
MindTheGap-2.2.3/ 0000775 0000000 0000000 00000000000 14060620177 0013501 5 ustar 00root root 0000000 0000000 MindTheGap-2.2.3/.gitignore 0000664 0000000 0000000 00000000056 14060620177 0015472 0 ustar 00root root 0000000 0000000 build*
test/output
.vscode/settings.json
*.pyc MindTheGap-2.2.3/.gitmodules 0000664 0000000 0000000 00000000155 14060620177 0015657 0 ustar 00root root 0000000 0000000 [submodule "thirdparty/gatb-core"]
path = thirdparty/gatb-core
url = https://github.com/GATB/gatb-core.git
MindTheGap-2.2.3/.travis.yml 0000664 0000000 0000000 00000001261 14060620177 0015612 0 ustar 00root root 0000000 0000000 language: cpp
os:
- linux
- osx
compiler:
- clang
- gcc
addons:
apt:
sources:
- ubuntu-toolchain-r-test
- llvm-toolchain-precise-3.7
- george-edison55-precise-backports # for cmake 3
packages:
- libcppunit-dev
- g++-4.8
- clang-3.7
- cmake
- cmake-data
install:
- if [ "`echo $CXX`" == "g++" ] && [ "$TRAVIS_OS_NAME" == "linux" ]; then export CXX=g++-4.8; fi
- if [ "`echo $CXX`" == "clang++" ] && [ "$TRAVIS_OS_NAME" == "linux" ]; then export CXX=clang++-3.7; fi
matrix:
exclude:
- os: osx
compiler: gcc
script:
- mkdir build
- cd build
- cmake .. && make
- cd ../test && ./simple_full_test.sh
env:
global:
- MAKEFLAGS="-j 4"
MindTheGap-2.2.3/CHANGELOG.md 0000664 0000000 0000000 00000013420 14060620177 0015312 0 ustar 00root root 0000000 0000000 # Change Log
--------------------------------------------------------------------------------
## [Unreleased]
--------------------------------------------------------------------------------
## [2.2.3] - 2021-06-11
* 2 novel options in the `Fill` (local assembly) module :
* `-fwd-only`: output the first-contig extensions of failed gap-fillings in a separate file, it can be useful for the assembly of the extremities of linear genomes (as in the [MinYS](https://github.com/cguyomar/MinYS) tool)
* `-extend`: do not try in reverse direction if no inserted sequence is assembled (bkpt mode), it can improve the running time and/or help the user controlling the direction of assembly (as in the [MTG-link](https://github.com/anne-gcd/MTG-Link) tool)
--------------------------------------------------------------------------------
## [2.2.2] - 2020-06-19
* A bug fix: updating gatb-core version, notably this fixes a bug in the `fill` module: nodes at extremities of contigs of size exactly `k` were not marked correctly, potentially leading to duplicated contigs in the contig graph. This could prevent exploring some parts of the graph, and if graph exploration parameters where set too large (`-max-nodes` and `-max-length`), it could lead in some rare cases to extreme running times and/or memory consumptions. This should no longer happen now.
--------------------------------------------------------------------------------
## [2.2.1] - 2019-11-29
* Some bug fixes:
* updating gatb-core version, notably this fixes a potentially important bug, where the de bruijn graph was erroneous for large datasets (such as human re-sequencing ones)
* bug fix in the fill module, node marking in contig graph construction was not working properly leading to obtain too many solutions, in the case of multiple solutions
* Some improvements:
* optimization of the algorithm to find paths in the fill module (should be faster);
* new options for insertion variant detection:
* `-bed` (find module): to limit the search of insertion breakpoint in specific regions.
* `-filter` (fill module): to remove insertions with multiple sequence solutions from the final vcf file (since they most often are a sign of false positive)
Note that the targeted assembly pipeline, including the gfa graph simplification scripts, is no longer included in this repository. This is now a proper tool, called MinYS (for MineYourSymbiont), which is distributed independently of MindTheGap and has now its own github repository : [https://github.com/cguyomar/MinYS](https://github.com/cguyomar/MinYS)
--------------------------------------------------------------------------------
## [2.2.0] - 2018-07-06
* A nice novel feature: insertion variants are now output in vcf format! and with left-normalization (ie. if several equivalent positions are possible for a given insertion event, the left-most is output and the size of the ambiguity is indicated).
* Some improvements and bug fixes:
* faster graph loading in fill module;
* if multiple inserted sequence solutions, better handling of very similar ones, the number of output solutions can be reduced;
* better handling of N stretches in the reference genome, resulting in less False Positive calls in find module;
* better recall for very small heterozygous insertion variants (bug fix when the insertion is size smaller or equal than the ambiguity size).
* a CI simple test for the Fill module with option `-contig`.
--------------------------------------------------------------------------------
## [2.1.0] - 2018-06-13
A nice novel feature:
MindTheGap can now also be used as a genome assembly finishing tool: it can fill the gaps between a set of input contigs without any a priori on their relative order and orientation. This new feature is available in the Fill module with option `-contig`.
Some bug and compilation fixes, by updating the gatb-core version to 1.4.1 and more.
--------------------------------------------------------------------------------
## [2.0.2] - 2017-07-06
Some new features:
* the Fill module is now parallelized and can use several cores
* additional information is output by the fill module:
* the abundance of each filled sequence is now computed and written in the fasta file
* a log file is output giving details about each gap-filling process
Bug fix:
* some gap-filled sequences were incorrect (this happened only for multiple filled sequences in rare cases)
--------------------------------------------------------------------------------
## [2.0.1] - 2016-07-21
This is a bug-fix release :
* fixed a compilation issue with old version of clang compilers (prior to clang 4.3 on mac), by updating the gatb-core version to 1.2.2.
--------------------------------------------------------------------------------
## [2.0.0] - 2016-06-29
* Initial release after refactoring the whole code of MindTheGap to use the **GATB library**.
Some of the benefits:
* faster (thanks to GATB improvements in kmer counting!);
* no longer need to recompile for changing the `k` parameter;
* automatic estimation of the paramater `abundance-min`;
* more user-friendly usage, with more readable help, progress bars, input-output summaries, etc.
* compatibility with other GATB tools: input-output graph in `h5` format.
* **New features** (with respect to the published version, August 2014):
* detection of homozygous SNPs and deletions (output in a separate VCF file); this should also improve the recall of insertion event detection;
* a quality score is now associated to each insertion prediction, this enables to filter out some predictions and to obtain a high-confidence subset.
Have a look at a comparison between the published and the 2.0.0 versions on simulated data [here](https://gatb.inria.fr/mindthegap-insertion-event-detection/).
MindTheGap-2.2.3/CMakeLists.txt 0000664 0000000 0000000 00000014171 14060620177 0016245 0 ustar 00root root 0000000 0000000 ################################################################################
# MindTheGap: Integrated detection and assembly of insertion variants
# A tool from the GATB (Genome Assembly Tool Box)
# Copyright (C) 2014 INRIA
# Authors: C.Lemaitre, G. Rizk
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see .
################################################################################
project(MindTheGap)
cmake_minimum_required(VERSION 3.1)
################################################################################
# The version number.
################################################################################
# The default version number is the latest official build
SET (gatb-tool_VERSION_MAJOR 2)
SET (gatb-tool_VERSION_MINOR 2)
SET (gatb-tool_VERSION_PATCH 3)
# But, it is possible to define another release number during a local build
IF (DEFINED MAJOR)
SET (gatb-tool_VERSION_MAJOR ${MAJOR})
ENDIF()
IF (DEFINED MINOR)
SET (gatb-tool_VERSION_MINOR ${MINOR})
ENDIF()
IF (DEFINED PATCH)
SET (gatb-tool_VERSION_PATCH ${PATCH})
ENDIF()
set (gatb-tool-version ${gatb-tool_VERSION_MAJOR}.${gatb-tool_VERSION_MINOR}.${gatb-tool_VERSION_PATCH})
# However, continuous integration has priority over local compilation
IF (DEFINED JENKINS_TAG)
SET (gatb-tool-version ${JENKINS_TAG})
ENDIF()
################################################################################
# Define cmake modules directory
################################################################################
SET (GATB_CORE_HOME ${PROJECT_SOURCE_DIR}/thirdparty/gatb-core/gatb-core)
SET (CMAKE_MODULE_PATH ${GATB_CORE_HOME}/cmake)
################################################################################
# SUPPORTED KMER SIZES
################################################################################
# One can uncomment this line and set the wanted values
#set (KSIZE_LIST "32 64 96 128 160 192 224 256")
################################################################################
# THIRD PARTIES
################################################################################
# We don't want to install some GATB-CORE artifacts
#SET (GATB_CORE_EXCLUDE_TOOLS 1)
SET (GATB_CORE_EXCLUDE_TESTS 1)
SET (GATB_CORE_EXCLUDE_EXAMPLES 1)
# GATB CORE
include (GatbCore)
################################################################################
# TOOL
################################################################################
# We also set a flag for TR1 management
if (use_new_cxx)
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DUSE_NEW_CXX ")
endif()
message("-- cxx: ${CMAKE_CXX_FLAGS}")
# we get compilation definitions from the gatb-core part
add_definitions (${gatb-core-flags})
# SET( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra" )
SET( CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -O0")
# we give the headers directories from :
# - from project source
# - from GATB-CORE source
# - from dsk source
set (PROGRAM_SOURCE_DIR ${PROJECT_SOURCE_DIR}/src)
include_directories (${PROGRAM_SOURCE_DIR} ${gatb-core-includes})
set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
# we define the files to be compiled
file (GLOB ProjectFiles src/*)
# we define the artifact to be built: the project binary
add_executable (${PROJECT_NAME} src/main.cpp ${ProjectFiles})
add_executable(nwalign src/nwAlign/nwalign.cpp)
# we define which libraries to be linked with project binary
target_link_libraries (${PROJECT_NAME} ${gatb-core-libraries})
target_link_libraries (nwalign ${gatb-core-libraries})
################################################################################
# PACKAGING
################################################################################
# We set the version number
SET (CPACK_PACKAGE_DESCRIPTION_SUMMARY "gatb-tool ${PROJECT_NAME}")
SET (CPACK_PACKAGE_VENDOR "Genscale team (INRIA)")
SET (CPACK_PACKAGE_VERSION_MAJOR "${gatb-tool_VERSION_MAJOR}")
SET (CPACK_PACKAGE_VERSION_MINOR "${gatb-tool_VERSION_MINOR}")
SET (CPACK_PACKAGE_VERSION_PATCH "${gatb-tool_VERSION_PATCH}")
SET (CPACK_PACKAGE_VERSION "${gatb-tool-version}")
# We set the kind of archive
SET (CPACK_GENERATOR "TGZ")
SET (CPACK_SOURCE_GENERATOR "TGZ")
# We ignore unwated files for the source archive
SET (CPACK_SOURCE_IGNORE_FILES
"^${PROJECT_SOURCE_DIR}/\\.git/" ;
"^${PROJECT_SOURCE_DIR}/\\.gitmodules" ;
"^${PROJECT_SOURCE_DIR}/\\.gitignore";
"^${PROJECT_SOURCE_DIR}/build/" ;
"^${GATB_CORE_HOME}/\\.cproject" ;
"^${GATB_CORE_HOME}/\\.git/" ;
"^${GATB_CORE_HOME}/\\.project" ;
"^${GATB_CORE_HOME}/\\.gitignore";
"^${GATB_CORE_HOME}/doc/design" ;
"^${GATB_CORE_HOME}/DELIVERY.md"
)
# We copy the project binary to the 'bin' directory
INSTALL (TARGETS ${PROJECT_NAME} DESTINATION bin)
INSTALL (DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/test DESTINATION .)
INSTALL (DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/data DESTINATION .)
#INSTALL (DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc DESTINATION .)
INSTALL (FILES ${CMAKE_CURRENT_SOURCE_DIR}/README.md DESTINATION .)
INSTALL (FILES ${CMAKE_CURRENT_SOURCE_DIR}/CHANGELOG.md DESTINATION .)
INSTALL (FILES ${CMAKE_CURRENT_SOURCE_DIR}/LICENSE DESTINATION .)
# We include the "bin" tag into binary archive file name
set (CPACK_PACKAGE_FILE_NAME ${PROJECT_NAME}-${CPACK_PACKAGE_VERSION}-bin-${CMAKE_SYSTEM_NAME})
include (CPack)
MindTheGap-2.2.3/INSTALL 0000664 0000000 0000000 00000001050 14060620177 0014526 0 ustar 00root root 0000000 0000000 # CMake is required to compile software (http://www.cmake.org/cmake/resources/software.html)
# you can install software by executing this file: sh INSTALL
#
# Prepare GATB sub-module
git submodule init
git submodule update
# Prepare directories:
rm -rf build
mkdir build
# Go in the 'build' directory
cd build
# Prepare the makefile
cmake ..
# Run the newly created makefile:
make
# To compile faster, use:
# make -j8
# Go back at the installation root directory
cd ..
# run tests
echo "Running simple test..."
cd test
. ./simple_test.sh
cd ..
MindTheGap-2.2.3/LICENSE 0000664 0000000 0000000 00000103330 14060620177 0014506 0 ustar 00root root 0000000 0000000 GNU AFFERO GENERAL PUBLIC LICENSE
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MindTheGap-2.2.3/README.md 0000664 0000000 0000000 00000032402 14060620177 0014761 0 ustar 00root root 0000000 0000000 # MindTheGap
| **Linux** | **Mac OSX** |
|-----------|-------------|
[](https://ci.inria.fr/gatb-core/view/MindTheGap/job/tool-mindthegap-build-debian7-64bits-gcc-4.7/) | [](https://ci.inria.fr/gatb-core/view/MindTheGap/job/tool-mindthegap-build-macos-10.9.5-gcc-4.2.1/)
[](http://bioconda.github.io/recipes/mindthegap/README.html)
[](http://www.gnu.org/licenses/agpl-3.0.en.html)
# What is MindTheGap ?
MindTheGap performs detection and assembly of **DNA insertion variants** in NGS read datasets with respect to a reference genome. It is designed to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome. It takes as input a set of reads and a reference genome. It outputs two sets of FASTA sequences: one is the set of breakpoints of detected insertion sites, the other is the set of assembled insertions for each breakpoint.
**New !** MindTheGap can also be used as a **genome assembly finishing tool**: it can fill the gaps between a set of input contigs without any a priori on their relative order and orientation. It outputs the results in a gfa file. It is notably integrated as an essential step in the targeted assembly tool **MinYS** (MineYourSymbiont in metagenomics datasets, see [https://github.com/cguyomar/MinYS](https://github.com/cguyomar/MinYS)).
MindTheGap is a [Genscale](http://team.inria.fr/genscale/) tool, built upon the [GATB](http://gatb.inria.fr/) C++ library, and developed by:
* Claire Lemaitre
* Cervin Guyomar
* Wesley Delage
* Guillaume Rizk
* Former developers: Rayan Chikhi, Pierre Marijon.
# Installation instructions
## Requirements
CMake 3.1+; see http://www.cmake.org/cmake/resources/software.html
C++/11 capable compiler (e.g. gcc 4.7+, clang 3.5+, Apple/clang 6.0+)
## Getting the latest source code with git
# get a local copy of MindTheGap source code
git clone --recursive https://github.com/GATB/MindTheGap.git
# compile the code
cd MindTheGap
sh INSTALL
# the binary file is located in directory build/bin/
./build/bin/MindTheGap -help
Note: when updating your local repository with `git pull`, if you see that thirdparty/gatb-core has changed, you have to run also : `git submodule update`.
## Installing a stable release
Retrieve a binary archive file from one of the official MindTheGap releases (see "Releases" tab on the Github web page); file name is `MindTheGap-vX.Y.Z-bin-Linux.tar.gz` (for Linux) or `MindTheGap-vX.Y.Z-bin-Darwin.tar.gz` (for MacOs).
tar -zxf MindTheGap-vX.Y.Z-bin-Darwin.tar.gz
cd MindTheGap-vX.Y.Z-bin-Darwin
chmod u+x bin/MindTheGap
./bin/MindTheGap -help
In case the software does not run appropriately on your system, you should consider to install it from its source code. Retrieve the source archive file `MindTheGap-vX.Y.Z-Source.tar.gz`.
tar -zxf MindTheGap-vX.Y.Z-Source.tar.gz
cd MindTheGap-vX.Y.Z-Source
sh INSTALL
# the binary file is located in directory build/bin/
./build/bin/MindTheGap -help
## Using conda or docker
MindTheGap is also distributed as a [Bioconda package](https://anaconda.org/bioconda/mindthegap):
conda install -c bioconda mindthegap
Or pull the docker image of MindTheGap (warning: need to be updated with latest releases):
docker pull clemaitr/mindthegap
## Small run example
```
MindTheGap find -in data/reads_r1.fastq,data/reads_r2.fastq -ref data/reference.fasta -out example
MindTheGap fill -graph example.h5 -bkpt example.breakpoints -out example
```
# USER MANUAL
## Description
MindTheGap is a software that performs integrated detection and assembly of **genomic insertion variants** in NGS read datasets with respect to a reference genome. It is designed to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome.
Alternatively and since release 2.1.0, MindTheGap can also be used as a **genome assembly finishing tool**. It is integrated as an essential step in the **targeted assembly** tool [MinYS (MineYourSymbiont in metagenomics datasets)](https://github.com/cguyomar/MinYS). It takes also part of a gap-filling pipeline dedicated to linked-read data (10X Genomics): [MTG-link](https://github.com/anne-gcd/MTG-Link).
**Insertion variant detection**
It takes as input a set of reads and a reference genome. Its main output is a VCF file, giving for each insertion variant, its insertion site location on the reference genome, a single insertion sequence or a set of candidate insertion sequences (when there are assembly ambiguities), and its genotype in the sample.
For a detailed user manual specific to insertion variants see [doc/MindTheGap_insertion_caller.md](doc/MindTheGap_insertion_caller.md).
**Genome assembly gap-filling** (New feature !)
When given a set of reads and a set of contigs as input, MindTheGap tries to fill the gaps between all pairs of contigs by de novo local assembly without any a priori on their relative order and orientation. It outputs the results in gfa file.
For a detailed user manual specific to contig gap-filling see [doc/MindTheGap_assembly.md](doc/MindTheGap_assembly.md).
**Performances**
MindTheGap performs de novo assembly using the [GATB](http://gatb.inria.fr) C++ library and inspired from algorithms from Minia. Hence, the computational resources required to run MindTheGap are significantly lower than that of other assemblers (for instance it uses less than 6GB of main memory for analyzing a full human NGS dataset).
For more details on the method and some recent results, see the [web page](http://gatb.inria.fr/software/mind-the-gap/).
## Usage and examples
MindTheGap is composed of two main modules : breakpoint detection (`find` module) and the local assembly of insertions or gaps (`fill` module). Both steps are implemented in a single executable, MindTheGap, and can be run independently by specifying the module name as follows :
MindTheGap [module options]
1. **Basic command lines**
#Find module:
MindTheGap find (-in | -graph ) -ref [options]
#To get help:
MindTheGap find -help
#Fill module:
MindTheGap fill (-in | -graph ) (-bkpt | -contig ) [options]
#To get help:
MindTheGap fill -help
2. **Examples**
These examples can be run with the small datasets in directory `data/`
**Example for insertion variant calling:**
#find
build/bin/MindTheGap find -in data/reads_r1.fastq,data/reads_r2.fastq -ref data/reference.fasta -out example
# 3 files are generated:
# example.h5 (de bruijn graph),
# example.othervariants.vcf (SNPs and deletion variants),
# example.breakpoints (breakpoints of insertion variants).
#fill
build/bin/MindTheGap fill -graph example.h5 -bkpt example.breakpoints -out example
# 3 files are generated:
# example.insertions.fasta (insertion sequences)
# example.insertions.vcf (insertion variants)
# example.info.txt (log file)
**Example for gap-filling between contigs:**
```
build/bin/MindTheGap fill -in data/contig-reads.fasta.gz -contig data/contigs.fasta -abundance-min 3 -out contig_example
# 4 files are generated
# contig_example.h5 (de bruijn graph)
# contig_example.insertions.fasta (gap-filling sequences)
# contig_example.gfa (genome graph)
# contig_example.info.txt (log file)
```
The usage of the `fill` module is a little bit different depending on the type of gap-filling : assembling insertion variants (using the `-bkpt`option with a breakpoint file) or gap-filling between contigs (using the `-contig` option with a contig fasta file).
## Details
1. **Input sequencing read data**
For both modules, read dataset(s) are first indexed in a De Bruijn graph. The input format of read dataset(s) is either the read files themselves (option `-in`), or the already computed de bruijn graph in hdf5 format (.h5) (option `-graph`).
NOTE: options `-in` and `-graph` are mutually exclusive, and one of these is mandatory.
If the input is composed of several read files, they can be provided as a list of file paths separated by a comma or as a "file of file" (fof), that is a text file containing on each line the path to each read file. All read files will be treated as if concatenated in a single sample. The read file format can be fasta, fastq or gzipped.
2. **de Bruijn graph creation options**
In addition to input read set(s), the de Bruijn graph creation uses two main parameters, `-kmer-size` and `-abundance-min`:
* `-kmer-size`: the k-mer size [default '31']. By default, the largest kmer-size allowed is 128. To use k>128, you will need to re-compile MindTheGap as follows:
```
cd build/
cmake -DKSIZE_LIST="32 64 96 256" ..
make
```
To go back to default, replace 256 by 128. Note that increasing the range between two consecutive kmer-sizes in the list can have an impact on the size of the output h5 files (but none on the results).
* `-abundance-min`: the minimal abundance threshold, k-mers having less than this number of occurrences are discarded from the graph [default 'auto', ie. automatically inferred from the dataset].
* `-abundance-max`: the maximal abundance threshold, k-mers having more than this number of occurrences are discarded from the graph [default '2147483647' ie. no limit].
3. **Computational resources options**
Additional options are related to computational runtime and memory:
* `-nb-cores`: number of cores to be used for computation [default '0', ie. all available cores will be used].
* `-max-memory`: max RAM memory for the graph creation (in MBytes) [default '2000']. Increasing the memory will speed up the graph creation phase.
* `-max-disk`: max usable disk space for the graph creation (in MBytes) [default '0', ie. automatically set]. Kmers are counted by writing temporary files on the disk, to speed up the counting you can increase the usable disk space.
4. **MindTheGap Output**
All the output files are prefixed either by a default name: "MindTheGap_Expe-[date:YY:MM:DD-HH:mm]" or by a user defined prefix (option `-out` of MindTheGap).
Both MindTheGap modules generate the graph file if reads were given as input:
* a graph file (`.h5`). This is a binary file, to obtain information stored in it, you can use the utility program `dbginfo` located in your bin directory or in ext/gatb-core/bin/.
`MindTheGap find` generates the following output files:
* a breakpoint file (`.breakpoints`) in fasta format.
* a variant file (`.othervariants.vcf`) in vcf format. It contains SNPs and deletion events.
`MindTheGap fill` generates the following output files:
* a sequence file (`.insertions.fasta`) in fasta format. It contains the inserted sequences or contig gap-fills that were successfully assembled.
* an insertion variant file (`.insertions.vcf`) in vcf format, in the case of insertion variant detection.
* an assembly graph file (`.gfa`) in GFA format, in the case of contig gap-filling. It contains the original contigs and the obtained gap-fill sequences (nodes of the graph), together with their overlapping relationships (arcs of the graph).
* a log file (`.info.txt`), a tabular file with some information about the filling process for each breakpoint/grap-fill.
* with option `-extend`, an additional sequence file (`.extensions.fasta`) in fasta format. It contains sequence extensions for failed insertion or gap-filling assemblies, ie. when the target kmer was not found, the first contig immediately after the source kmer is output.
Other optional parameters and details on input and output file formats are given in [doc/MindTheGap_insertion_caller.md](doc/MindTheGap_insertion_caller.md) and [doc/MindTheGap_assembly.md](doc/MindTheGap_assembly.md), depending on the usage.
## Utility programs
Either in your `bin/` directory or in `ext/gatb-core/bin/`, you can find additional utility programs :
* `dbginfo` : to get information about a graph stored in a .h5 file
* `dbgh5` : to build a graph from read set(s) and obtain a .h5 file
* `h5dump` : to extract data stored in a .h5 file
## Reference
MindTheGap: integrated detection and assembly of short and long insertions. Guillaume Rizk, Anaïs Gouin, Rayan Chikhi and Claire Lemaitre. Bioinformatics 2014 30(24):3451-3457. http://bioinformatics.oxfordjournals.org/content/30/24/3451
[Web page](https://gatb.inria.fr/software/mind-the-gap/) with some updated results.
# Contact
To contact a developer, request help, or for any feedback on MindTheGap, please use the issue form of github: https://github.com/GATB/MindTheGap/issues
You can see all issues concerning MindTheGap [here](https://github.com/GATB/MindTheGap/issues) and GATB [here](https://www.biostars.org/t/GATB/).
If you do not have any github account, you can also send an email to claire dot lemaitre at inria dot fr
MindTheGap-2.2.3/container/ 0000775 0000000 0000000 00000000000 14060620177 0015463 5 ustar 00root root 0000000 0000000 MindTheGap-2.2.3/container/Dockerfile 0000664 0000000 0000000 00000001531 14060620177 0017455 0 ustar 00root root 0000000 0000000 FROM debian:wheezy
MAINTAINER Claire Lemaitre claire.lemaitre@inria.fr
# Set MindTheGap version
ENV MTG_VERSION 2.1.0
# Set noninteratve mode
ENV DEBIAN_FRONTEND noninteractive
ENV PACKAGES wget gcc g++ make cmake zlib1g-dev libboost-dev git
ENV DIR /opt
ENV SOURCE MindTheGap
ENV BUILD build
WORKDIR ${DIR}
RUN apt-get update -y && \
apt-get install -y --no-install-recommends ${PACKAGES}
RUN git config --global http.sslVerify false
# clone the github repo
RUN git clone --recursive https://github.com/GATB/MindTheGap.git
WORKDIR ${DIR}/${SOURCE}
RUN git submodule init
# Using an official release
RUN git checkout v${MTG_VERSION}
RUN git submodule update
RUN mkdir ${BUILD}
WORKDIR ${DIR}/${SOURCE}/${BUILD}
RUN cmake ..
RUN make
# symlink binary in /usr/local/bin
RUN ln -s ${DIR}/${SOURCE}/${BUILD}/bin/MindTheGap /usr/local/bin
MindTheGap-2.2.3/container/MTG_recipes 0000664 0000000 0000000 00000001647 14060620177 0017557 0 ustar 00root root 0000000 0000000 Bootstrap: docker
From: ubuntu:16.04
%environment
export PATH="$PATH:/opt/MindTheGap/build/ext/gatb-core/bin"
%post
apt-get -y update && \
apt-get install -y --no-install-recommends \
wget \
gcc \
g++ \
make \
cmake \
zlib1g-dev \
libboost-dev \
bzip2 \
python2.7 \
default-jre \
libbz2-dev \
liblzma-dev \
default-jdk \
python3 \
python3-pip \
cython \
unzip \
git;\
git config --global http.sslVerify false;\
cd /opt;\
git clone --recursive https://github.com/GATB/MindTheGap.git;\
cd MindTheGap;\
git submodule init;\
git submodule update;\
mkdir build;\
cd build;\
cmake ..;\
make;\
cd ..;\
git config --global http.sslVerify false;\
pip3 install pyGATB;\
pip3 install biopython;\
pip3 install pandas;\
pip3 install numpy;\
MindTheGap-2.2.3/container/README.txt 0000664 0000000 0000000 00000000406 14060620177 0017161 0 ustar 00root root 0000000 0000000 MTG_recipes is a recipe to build MindTheGap master version using singularity. The recipe contains python2 and python3(pyGATB,biopython,pandas and numpy installed)
To build MindTheGap image use the command:
sudo singularity build Name_my_image.sif MTP_recipes
MindTheGap-2.2.3/data/ 0000775 0000000 0000000 00000000000 14060620177 0014412 5 ustar 00root root 0000000 0000000 MindTheGap-2.2.3/data/contig-reads.fasta.gz 0000664 0000000 0000000 00000604042 14060620177 0020436 0 ustar 00root root 0000000 0000000 -?[ reads.fasta ̽Ɏdɒχ!l6
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