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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
SAMTools Manipulating alignments in the SAM format (sorting, merging, indexing and ...) The software is free and is designed for multiple uses.
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
ERANGE (RNA-Seq) ERANGE is a python package and uses the Cistematic package The software is free and gives the flexible input parameter choice
Illumina (RNA-Seq) Counts can be visualized and analyzed in Illumina's GenomeStudio viewer License required, more robust (requires Illumina's output directory contents)
TopHat Fast splice junction mapper Input files can be either FASTQ or FASTA format
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
ERANGE (Chip-Seq) Studying protein-DNA interactions Free
HPeak The software can accurately pinpoint regions to which significantly more sequence reads are mapped Hidden Markov model-based approach
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.
CISGenome An integrated tool for tiling arrays, ChIP-seq, genome and cis-regulatory element analysis N.A.