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

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

Manipulating alignments in the SAM format (sorting, merging, indexing and ...)

The software is free and is designed for multiple uses.

http://samtools.sourceforge.net/

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 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/

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/

Fast splice junction mapper

Input files can be either FASTQ or FASTA format

http://tophat.cbcb.umd.edu/

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/

Studying protein-DNA interactions

Free

http://woldlab.caltech.edu/erange/README.chip-seq

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/

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/

An integrated tool for tiling arrays, ChIP-seq, genome and cis-regulatory element analysis

N.A.

http://www.biostat.jhsph.edu/~hji/cisgenome/