Stars
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A versatile pairwise aligner for genomic and spliced nucleotide sequences
MMseqs2: ultra fast and sensitive search and clustering suite
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
De novo assembler for single molecule sequencing reads using repeat graphs
Short read de novo assembler using de Bruijn graphs, as published in: D.R. Zerbino and E. Birney. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research, 1…
MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics
sensitive and precise assembly of short sequencing reads
A fork of Prodigal meant to improve gene calling for giant viruses and viruses that use alternative genetic codes