Analyse de variants
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.
|Run Unix # java -jar /usr/local/genome/gatk/GenomeAnalysisTK.jar -h||Run Web #|
GRIL is a tool to detect the locations of genomic rearrangements in a set of sequences.
|Run Unix # gril||Run Web #|
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.
|Run Unix # novosnp2.0.1||Run Web #|
This software package infers population size history from a diploid sequence using the Pairwise Sequentially Markovian Coalescent (PSMC) model.
|Run Unix # psmc [options] input.txt||Run Web #|
SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
|Run Unix # samtools ||Run Web #|
A C++ library for parsing and manipulating VCF files.
|Run Unix #||Run Web #|