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