Table 2.

Widely used open source softwares for bioinformatics analysis of NGS data

Module and specific tool	Website link
Quality control analysis
FastQC	https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
NGS QC Toolkit	http://www.nipgr.res.in/ngsqctoolkit.html
Pre‐processing of reads
Trimmomatic	http://www.usadellab.org/cms/?page=trimmomatic
FASTX‐Toolkit	http://hannonlab.cshl.edu/fastx_toolkit/
Alignment to reference genome
Bowtie2	http://bowtie-bio.sourceforge.net/ bowtie2/ index.shtml
BWA MEM	http://bio-bwa.sourceforge.net/
Stampy	http://www.well.ox.ac.uk/project-stampy
Removal of duplicate reads
Picard (Markduplicates)	http://broadinstitute.github.io/picard/
Samtools (rmdup)	http://samtools.sourceforge.net/
Indel realignment
GATK (IndelRealignment)	https://software.broadinstitute.org/gatk/
Genotyping
GATK (HaplotypeCaller/UnifiedCaller)	https://software.broadinstitute.org/gatk/
Samtools (mpileup)	http://samtools.sourceforge.net/
Recombination analysis
ReCombine	https://sourceforge.net/projects/recombine/
Statistical analysis and visualization
R	https://www.r-project.org/
IGV	http://software.broadinstitute.org/software/igv/