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Burrows-Wheeler Aligner (BWA) is one of the most popular short sequence aligners for nongapped aligning analysis. BWA scales well until 32 cores, and CPU usage drops down 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. Sambamba 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 toolkit to identify SNPs, indels, copy number variation (CNV), and structural variation (SV) in germline and somatic DNAseq and RNAseq data. It also includes many utilities to perform related tasks.