Packages
C/C++ genomics tools available as WebAssembly modules
samtools
Parse and manipulate .sam
/ .bam
read alignment files
bcftools
Parse and manipulate .vcf
/ .bcf
variant calling files
bedtools
Parse .bed
files and perform complex "genome arithmetic"
bowtie2
Align sequencing reads (.fastq
) files to a reference genome
minimap2
Align sequencing reads (.fastq
) files to a reference genome
fastp
Manipulate and evaluate QC of .fastq
files
seqtk
Manipulate and evaluate QC of .fasta
/ .fastq
files
wgsim
Simulate short reads from a reference genome
v2011.10.17seq-align
Align sequences to each other using the Smith-Waterman and Needleman-Wunsch algorithms
v2017.10.18ssw
A SIMD-based implementation of the Smith-Waterman (requires enabling the WebAssembly SIMD flag in browser)
v1.2.4bhtsne
Run the t-SNE dimensionality-reduction algorithm
v2016.08.22jq
Filter and wrangle JSON strings
v1.6iVar
Tools for viral amplicon-based sequencing
v1.3.1modbam2bed
Summarize BAM files containing modified-base information to BED formatted counts
v0.3.1gawk
Manipulate data files with patterns of interest
v5.1.0kalign
Multiple sequence alignment
v3.3.1FastTree
Phylogenetic trees from multiple sequence alignments
v2.1.11tabix
Index and parse tab-delimited genome position files
v1.10htsfile
Identify the type of sequencing data file
v1.10bgzip
Block compression/decompression
v1.10grep
Find patterns in files
v3.7sed
Search and replace utility
v4.8