| Version | MAJ | gatk | ||
| 3.5 | 2016-01-25 | Download | Doc |
The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyze high-throughput sequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Remarque
| Run Unix # java -jar /usr/local/genome/gatk/GenomeAnalysisTK.jar -h | Run Web # |
| Version | MAJ | gril | ||
| 1.0.0 | Download | Doc |
GRIL is a tool to detect the locations of genomic rearrangements in a set of sequences.
Remarque
| Run Unix # gril | Run Web # |
| Version | MAJ | novosnp | ||
| 2.0.1 | Download | Doc |
novoSNP is a program that will help you find variations (SNPs and short INDELs) in resequencing projects. It takes a reference sequence and a number of sequencing trace files as input, and generates a list of possible variations with a quality score. novoSNP allows you to easily filter, sort and check the variations found visually and keep track of your verifications.
Remarque
| Run Unix # novosnp2.0.1 | Run Web # |
| Version | MAJ | PSMC | ||
| 0.6.5 | 2016-04-07 | Download | Doc |
This software package infers population size history from a diploid sequence
using the Pairwise Sequentially Markovian Coalescent (PSMC) model.
Remarque
| Run Unix # psmc [options] input.txt | Run Web # |
| Version | MAJ | SAMtools | ||
| 1.2 | 2015-04-15 | Download | Doc |
SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
Remarque
| Run Unix # samtools | Run Web # |
| Version | MAJ | Vcflib | ||
| 2017-03-10 | Download | Doc |
A C++ library for parsing and manipulating VCF files.
Remarque
| Run Unix # | Run Web # |
