Burrows-Wheeler Aligner (BWA) is one of the most popular short sequence aligners for non-gapped aligning analysis. BWA scales well up to 32 cores, and CPU usage drops dramatically after 32 cores. The runtime improvement becomes marginal with higher core numbers greater than 32.
Sambamba is a highly parallel tool for working with SAM, BAM, and CRAM sequence alignment files. This is a faster alternative to Samtools and Picard. Sambamba is used to sort alignment results from BWA.
Samtools is a suite of programs for interacting with high-throughput sequencing data.
Genome Analysis Toolkit (GATK) is a tool kit to identify SNPs, indels, copy number variation (CNV), and structural variation (SV) in germline and somatic DNA-seq and RNA-seq data. It also includes many utilities to perform related tasks.
