| 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 |
| 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 |