DIAMOND

Burrow-Wheeler Aligner for pairwise alignment between DNA sequences.

Freely available tools for biological computing in Python, with included cookbook, packaging and thorough documentation. Part of the [Open Bioinformatics Foundation](http://open-bio.org/). Contains the very useful [Entrez](https://biopython.org/DIST/docs/api/Bio.Entrez-module.html) package for API access to the NCBI databases.

Minimap2 is an pairwise aligner for genomic and spliced nucleotide sequences. It can perform the assembly-to-assembly alignment, and works with gzip'd FASTQ, FASTA formats. It also finds overlaps between long-reads.

An ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.

Java framework for processing biological data.

A system for rapidly aligning entire genomes, whether in complete or draft form.