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Table 2 Selected variant calling, RNA-Seq, and ChIP-Seq software/tools and database links

From: Current status and future perspectives for sequencing livestock genomes

Name Description Features/Restrictions Link
SNVMix Detects single nucleotide variants from next generation sequencing data Input files are Maq or Samtools pileup format http://www.bcgsc.ca/platform/bioinfo/software/SNVMix
SAMTools Manipulating alignments in the SAM format (sorting, merging, indexing and ...) The software is free and is designed for multiple uses. http://samtools.sourceforge.net/
GATK Contains modules of depth of coverage analyzers, quality score recalibrator, SNP/Indel caller, and local realigner The software is Java based and requires input files as sorted, indexed BAM alignment files and a fasta-format reference with associated index files http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit
ERANGE (RNA-Seq) ERANGE is a python package and uses the Cistematic package The software is free and gives the flexible input parameter choice http://woldlab.caltech.edu/rnaseq/
Illumina (RNA-Seq) Counts can be visualized and analyzed in Illumina's GenomeStudio viewer License required, more robust (requires Illumina's output directory contents) http://www.illumina.com/
TopHat Fast splice junction mapper Input files can be either FASTQ or FASTA format http://tophat.cbcb.umd.edu/
Cufflinks Assembling transcripts and estimating their abundances from RNA-Seq data Input alignment files are in the SAM format and the software requires reference annotation GTF file http://cufflinks.cbcb.umd.edu/
ERANGE (Chip-Seq) Studying protein-DNA interactions Free http://woldlab.caltech.edu/erange/README.chip-seq
HPeak The software can accurately pinpoint regions to which significantly more sequence reads are mapped Hidden Markov model-based approach http://www.sph.umich.edu/csg/qin/HPeak/
MACS Uses a dynamic Poisson distribution to effectively capture local biases in the genome sequence and allows for more sensitive and robust prediction The software is publicly available open-source, and used for ChIP-Seq analysis with or without control samples. http://liulab.dfci.harvard.edu/MACS/
CISGenome An integrated tool for tiling arrays, ChIP-seq, genome and cis-regulatory element analysis N.A. http://www.biostat.jhsph.edu/~hji/cisgenome/