Table 3.

List of various tools used during NGS pipeline analysis

Tools	Description	URL	References
Quality control (QC)
FastQC	A QC tool for high-throughput data	https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
RnBeads	A QC tool for DNA methylation data	https://rnbeads.org/	(114)
Meffil	A QC tool specifically designed to handle gigantic DNA methylation data	https://github.com/perishky/meffil/	(115)
Alignment
BWA	Alignment tool for mapping low-divergent sequences	http://bio-bwa.sourceforge.net/bwa.shtml	(116)
Hisat2	Alignment tool for RNA-seq reads	https://github.com/DaehwanKimLab/hisat2/blob/master/docs/_data/collaborate.yml	(117)
Bowtie	Ultra-fast, memory efficient short read aligner	http://bowtie.cbcb.umd.edu/	(118)
DNAscan	fast and efficient bioinformatics pipeline that allows for the analysis of DNA Next Generation sequencing data, requiring very little computational effort and memory usage.	https://github.com/KHP-Informatics/DNAscan	(119)
Variant calling
SAMtools	Variant calling tool which is based on UNIX commands	https://samtools.github.io/bcftools/howtos/variant-calling.html	(120)
GATK	A genome analysis toolkit for variant detection	https://gatk.broadinstitute.org/hc/en-us	(121)
SNVer	A statistical tool for calling rare variant in analyzing poor or individual NGS data	https://sourceforge.net/projects/snver/	(122)
Annotation
ANNOVAR	A tool for functionally annotating genetic variants	https://annovar.openbioinformatics.org/en/latest/user-guide/filter/	(123)
SAVANT	Sequence annotation and visualization analysis tool for genomic data	http://compbio.cs.toronto.edu/savant	(124)
SVA	NGS tool for annotating and visualizing human genomic data	https://www.ebi.ac.uk/ena/browser/sva	(125)
VariantDB	A flexible annotation and filtering tool for NGS data	http://www.biomina.be/app/variantdb/	(126)