Next-generation sequencing (NGS), also known as high-throughput sequencing, is the catch-all term used to describe a number of different modern sequencing technologies. These technologies allow for sequencing of DNA and RNA much more quickly and cheaply than the previously used Sanger sequencing, and as such revolutionised the study of genomics and molecular biology.

ANNOVAR
Functionally annotate genetic variants detected from diverse genomes. BamTools
Toolkit for handling BAM files bcftools
Utilities for variant calling and manipulating VCFs and BCFs. bcl2fastq
bcl2fastq converts BCL files to fastq files bcl-convert
Convert Binary Base Call (BCL) to FASTQ files bedops
BEDOPS is a suite of tools to address common questions raised in genomic studies. bedtools
bedtools utilities are a swiss-army knife of tools bowtie
Bowtie1 is a fast, multi-threaded, and memory efficient aligner for short read sequences. bowtie2
Bowtie2 is a fast, multi-threaded, and memory efficient aligner for short read sequences. bwa
BWA aligns short sequences to a sequence database htslib
HTSlib is an implementation of a unified C library for accessing common file formats. samtools
Samtools is a suite of programs for interacting with high-throughput sequencing data.