Bowtie is an ultrafast, memory-efficient short read aligner.

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning read

Burrow-Wheeler Aligner for pairwise alignment between DNA sequences

Fast, accurate, memory-efficient aligner for short and long sequencing reads

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Disambiguating two species in next generation sequencing data from grafted samples. Operates on DNA or RNA-seq alignments to the two species and separ

A software package with various utilities for processing alignments in the SAM format, including variant calling and alignment viewing.

Subread is a general-purpose read aligner which can be used to map both genomic DNA-seq reads and RNA-seq reads. It uses a new mapping paradigm called