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 2.31.0 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
cawlign Align/map sequences in a FASTA file to a reference sequence in a codon-aware manner 0.1.0 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
findutils Search for files in a folder 4.9.0 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
gfatools Tools for manipulating pangenome sequence graphs 253 0
gffread Parse and file .gff/.gtf files 0.12.7 0
grep Search and filter files 3.7 0
htslib Bioinformatics file format utilities: tabix, htsfile, and bgzip 1.17 0
hyphy Comparative sequence analysis using stochastic evolutionary models 2.5.57 0
ivar Tools for viral amplicon-based sequencing 1.3.1 0
jq Filter and wrangle JSON strings 1.7 0
kalign Multiple sequence alignment 3.3.1 0
kentutils File conversion utilities 437 0
libarchive Unzip .zip files 3.7.2 0
lsd2 A phylogeny dating method 2.3 0
mafft Multiple sequence alignment for amino acid or nucleotide sequences 7.520 0
minimap2 Pairwise sequence alignment 2.22 0
modbam2bed Summarize .bam modified bases as .bed files with counts 0.9.5 0
muscle Multiple alignments of biological sequences 5.1.0 0
samtools Parse .sam / .bam read alignment files 1.17 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 1.4 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 1.0.11 0
tree List folder contents in a tree format 2.0.4 0
ViralConsensus Call viral consensus genomes from read alignments 0.0.5 0
wgsim Simulate short reads from a reference genome 2011.10.17 0