GATB/gatb-minia-pipeline

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Language
Perl
Created about 9 years ago
Updated almost 2 years ago

GATB/gatb-minia-pipeline

GATB

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GATB Minia assembly pipeline

bcalm

compacted de Bruijn graph construction in low memory

minia

Minia is a short-read assembler based on a de Bruijn graph

gatb-core

Core library of the Genome Analysis Toolbox with de-Bruijn graph

simka

Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.

dsk

k-mer counting software

DiscoSnp

DiscoSnp is designed for discovering all kinds of SNPs (not only isolated ones), as well as insertions and deletions, from raw set(s) of reads.

MindTheGap

MindTheGap is a SV caller for short read sequencing data dedicated to insertion variants (all sizes and types). It can also be used as a local assembly tool.

bloocoo

Bloocoo is a k-mer spectrum-based read error corrector, designed to correct large datasets with a very low memory footprint.

pyGATB

Python3 wrapper for GATB-Core.

leon

Leon - FASTA and FASTQ read compressor

short_read_connector

Short Read Connector (SRC)

TakeABreak

TakeABreak detects inversion breakpoints in read datasets without a reference genome

tigops

Manipulation of unitigs and contigs

gatb-tools-machine

Build a single Docker image containing all GATB-Tools ready to be used. This is an official repository, not a mirror.

gatb-core-tuto

This project hosts the source code of the GATB-Core Programming Online Tutorial.