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bioinformatics
sequencing
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|
| Package |
Description |
Version |
|
abpoa
☆
formula
|
SIMD-based C library for fast partial order alignment using adaptive band |
1.5.5 |
|
abricate
☆
formula
|
Find antimicrobial resistance and virulence genes in contigs |
1.2.0 |
|
abyss
☆
formula
|
Genome sequence assembler for short reads |
2.3.10 |
|
adapterremoval
☆
formula
|
Rapid adapter trimming, identification, and read merging |
2.3.4 |
|
augustus
☆
formula
|
Predict genes in eukaryotic genomic sequences |
3.5.0 |
|
autocycler
☆
formula
|
Tool for generating consensus long-read assemblies for bacterial genomes |
0.5.2 |
|
badread
☆
formula
|
Long read simulator that can imitate many types of read problems |
0.4.1 |
|
bamtools
☆
formula
|
C++ API and command-line toolkit for BAM data |
2.5.3 |
|
bandage
☆
cask
|
Bioinformatics app for navigating de novo assembly graphs |
0.9.0 |
|
bbtools
☆
formula
|
Brian Bushnell's tools for manipulating reads |
39.59 |
|
bcftools
☆
formula
|
Tools for BCF/VCF files and variant calling from samtools |
1.23 |
|
bedops
☆
formula
|
Set and statistical operations on genomic data of arbitrary scale |
2.4.42 |
|
bedtk
☆
formula
|
Simple toolset for BED files |
1.2 |
|
bedtools
☆
formula
|
Tools for genome arithmetic (set theory on the genome) |
2.31.1 |
|
bioawk
☆
formula
|
AWK modified for biological data |
1.0 |
|
bioperl
☆
formula
|
Perl tools for bioinformatics, genomics and life science |
1.7.8 |
|
blast
☆
formula
|
Basic Local Alignment Search Tool |
2.17.0 |
|
bowtie2
☆
formula
|
Fast and sensitive gapped read aligner |
2.5.4 |
|
breseq
☆
formula
|
Computational pipeline for finding mutations in short-read DNA resequencing data |
0.39.0 |
|
btllib
☆
formula
|
Bioinformatics Technology Lab common code library |
1.7.5 |
|
bwa
☆
formula
|
Burrow-Wheeler Aligner for pairwise alignment of DNA |
0.7.19 |
|
diamond
☆
formula
|
Accelerated BLAST compatible local sequence aligner |
2.1.16 |
|
fastga
☆
formula
|
Pairwise whole genome aligner |
1.3.1 |
|
fastk
☆
formula
|
K-mer counter for high-fidelity shotgun datasets |
1.1.0 |
|
fastp
☆
formula
|
Ultra-fast all-in-one FASTQ preprocessor |
1.0.1 |
|
fastq-tools
☆
formula
|
Small utilities for working with fastq sequence files |
0.8.3 |
|
fastqc
☆
formula
|
Quality control tool for high throughput sequence data |
0.12.1 |
|
fgbio
☆
formula
|
Tools for working with genomic and high throughput sequencing data |
|
|
flye
☆
formula
|
De novo assembler for single molecule sequencing reads using repeat graphs |
|
|
freebayes
☆
formula
|
Bayesian haplotype-based genetic polymorphism discovery and genotyping |
|
|
geneious-prime
☆
cask
|
Bioinformatics software platform |
2026.0.2 |
|
genometools
☆
formula
|
Versatile open source genome analysis software |
1.6.6 |
|
gffread
☆
formula
|
GFF/GTF format conversions, region filtering, FASTA sequence extraction |
|
|
hmmer
☆
formula
|
Build profile HMMs and scan against sequence databases |
|
|
htslib
☆
formula
|
C library for high-throughput sequencing data formats |
|
|
igv
☆
cask
|
Visual exploration of genomic data |
2.18.0 |
|
igv
☆
formula
|
Interactive Genomics Viewer |
2.19.7 |
|
igv-desktop
☆
cask
|
Visual exploration of genomic data |
2.19.7 |
|
jalview
☆
cask
|
Multiple sequence alignment editor, visualiser, analysis and figure generator |
2.11.5.1 |
|
jbrowse
☆
cask
|
Genome browser |
4.1.3 |
|
jellyfish
☆
formula
|
Fast, memory-efficient counting of DNA k-mers |
|
|
kalign
☆
formula
|
Fast multiple sequence alignment program for biological sequences |
|
|
kallisto
☆
formula
|
Quantify abundances of transcripts from RNA-Seq data |
|
|
kraken2
☆
formula
|
Taxonomic sequence classification system |
2.17.1 |
|
lastz
☆
formula
|
Pairwise aligner for DNA sequences |
|
|
mafft
☆
formula
|
Multiple alignments with fast Fourier transforms |
|
|
minigraph
☆
formula
|
Proof-of-concept seq-to-graph mapper and graph generator |
|
|
minimap2
☆
formula
|
Versatile pairwise aligner for genomic and spliced nucleotide sequences |
|
|
miniprot
☆
formula
|
Align proteins to genomes with splicing and frameshift |
|
|
mmseqs2
☆
formula
|
Software suite for very fast sequence search and clustering |
18-8cc5c |