Name Description Latest Downloads
aioli JavaScript library for running biowasm tools 3.1.0 0
bcftools Parse .vcf / .bcf variant calling files 1.10 0
bedtools Parse .bed files and perform complex genome arithmetic 2.29.2 0
bhtsne Run the t-SNE dimensionality-reduction algorithm 2016.08.22 0
bowtie2 Align sequencing reads (.fastq) files to a reference genome 2.4.2 0
coreutils Bash utilities such as head, tail, ls, sort, uniq, etc. 8.32 0
fastp Evaluate data quality of .fastq files 0.20.1 0
fasttree Build phylogenetic trees from multiple sequence alignments 2.1.11 0
gawk Manipulate data files with patterns of interest 5.1.0 0
grep Search and filter files 3.7 0
htslib Bioinformatics file format utilities: tabix, htsfile, and bgzip 1.10 0
ivar Tools for viral amplicon-based sequencing 1.3.1 0
jq Filter and wrangle JSON strings 1.6 0
kalign Multiple sequence alignment 3.3.1 0
lsd2 A phylogeny dating method 2.3 0
minimap2 Pairwise sequence alignment 2.22 0
modbam2bed Summarize .bam modified bases as .bed files with counts 0.3.1 0
samtools Parse .sam / .bam read alignment files 1.10 0
sed Find and replace utilities 4.8 0
seq-align Align sequences using Smith-Waterman/Needleman-Wunsch 2017.10.18 0
seqtk Parse and wrangle .fasta / .fastq files 1.3 0
ssw A SIMD implementation of the Smith-Waterman algorithm 1.2.4 0
tn93 Pairwise distance on FASTA files using Tamura Nei 93 distance 1.0.9 0
wgsim Simulate short reads from a reference genome 2011.10.17 0