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psm-utils
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public |
Common utilities for parsing and handling peptide-spectrum matches and search engine results.
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2025-03-06 |
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tower-cli
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public |
The Tower CLI an interface to Nextflow Tower via the CLI
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2025-03-06 |
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gfastats
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public |
The swiss army knife for genome assembly
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2025-03-06 |
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methbat
|
public |
A battery of methylation tools for PacBio HiFi reads
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2025-03-06 |
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tb-profiler
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public |
Profiling tool for Mycobacterium tuberculosis to detect drug resistance and lineage from sequencing data
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2025-03-06 |
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enviroampdesigner
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public |
Tool for training model and classifying reads from environmental ONT amplicon sequencing.
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2025-03-06 |
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autocycler
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public |
A tool for generating consensus long-read assemblies for bacterial genomes.
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2025-03-06 |
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vuegen
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public |
VueGen automates the creation of reports from bioinformatics outputs, supporting formats like PDF, HTML, DOCX, ODT, PPTX, Reveal.js, Jupyter notebooks, and Streamlit web applications. Users simply provide a directory with output files—such as plots, tables, networks, Markdown text, and HTML files—and VueGen compiles them into a structured report.
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2025-03-05 |
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fast2q
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public |
A Python3 program that counts sequence occurrences in FASTQ files.
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2025-03-05 |
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pigpen
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public |
A package to quantify RNA localization using OINC-seq data
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2025-03-05 |
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hictk
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public |
Blazing fast toolkit to work with .hic and .cool files
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2025-03-05 |
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bwa-mem2
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public |
The next version of bwa-mem
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2025-03-05 |
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rust-gtars
|
public |
Performance-critical tools to manipulate, analyze, and process genomic interval data.
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2025-03-05 |
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eastr
|
public |
Tool for emending alignments of spuriously spliced transcript reads.
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2025-03-05 |
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snakemake-storage-plugin-sharepoint
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public |
Snakemake storage plugin for reading and writing files on Microsoft SharePoint.
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2025-03-05 |
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varlociraptor
|
public |
Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control.
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2025-03-05 |
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kmercamel
|
public |
KmerCamel🐫 - compressing k-mer sets using masked superstrings
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2025-03-05 |
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r-tinyarray
|
public |
Gene Expression Omnibus(GEO) and The Cancer Genome Atlas(TCGA) are common bioinformatics public databases. We integrate the regular analysis and charts for expression data, to analyze and display the data concisely and intuitively.
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2025-03-05 |
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ebi-eva-common-pyutils
|
public |
EBI EVA - Common Python Utilities
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2025-03-05 |
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argnorm
|
public |
Normalize antibiotic resistance genes (ARGs) abundance tables (e.g., from metagenomics) by using the ARO ontology (developed by CARD).
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2025-03-05 |
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bam-readcount
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public |
bam-readcount generates metrics at single nucleotide positions.
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2025-03-05 |
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quantms-rescoring
|
public |
PSM rescoring python package with scripts and helpers for the quantms workflow
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2025-03-05 |
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simpleaf
|
public |
A rust framework to make using alevin-fry even simpler.
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2025-03-05 |
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reseek
|
public |
Protein structure alignment and search algorithm.
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2025-03-05 |
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sylph-tax
|
public |
Integrating taxonomic information into the sylph metagenome profiler.
|
2025-03-05 |
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dnaapler
|
public |
Reorients assembled microbial sequences
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2025-03-05 |
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nextflow
|
public |
A DSL for data-driven computational pipelines http://nextflow.io
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2025-03-04 |
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pyopal
|
public |
Cython bindings and Python interface to Opal, a SIMD-accelerated pairwise aligner.
|
2025-03-04 |
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cayman
|
public |
A command-line profiling tool for profiling CAZyme abundances in metagenomic datasets.
|
2025-03-04 |
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stranger
|
public |
Annotate VCF files with STR variants with pathogenicity implications.
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2025-03-04 |
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picrust2
|
public |
PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States
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2025-03-04 |
|
ngscheckmate
|
public |
Software package for identifying next generation sequencing (NGS) data files from the same individual.
|
2025-03-04 |
|
superintervals
|
public |
Rapid interval intersections
|
2025-03-04 |
|
piawka
|
public |
The powerful AWK script to calculate population statistics in VCF files with support for varying ploidy and missing data
|
2025-03-04 |
|
atlas
|
public |
ATLAS: Analysis Tools for Ancient and Low-depth Samples
|
2025-03-04 |
|
rnalyze
|
public |
A comprehensive pipeline for RNA-Seq data analysis.
|
2025-03-04 |
|
egap
|
public |
EGAP pipeline for genome assembly and QC analysis
|
2025-03-04 |
|
amplicontyper
|
public |
Tool for training model and classifying reads from environmental ONT amplicon sequencing.
|
2025-03-04 |
|
mity
|
public |
Mity is a bioinformatic analysis pipeline designed to call mitochondrial SNV and INDEL variants from Whole Genome Sequencing (WGS) data.
|
2025-03-04 |
|
taxor
|
public |
Fast and space-efficient taxonomic classification of long reads
|
2025-03-04 |
|
pfam_scan
|
public |
pfam_scan.pl is a Perl script calling HMMER v3 to search a FASTA file against a library of Pfam HMMs.
|
2025-03-04 |
|
frogs
|
public |
FROGS is a workflow designed to metabarcoding sequence analysis
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2025-03-04 |
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pyfamsa
|
public |
Cython bindings and Python interface to FAMSA, an algorithm for ultra-scale multiple sequence alignments.
|
2025-03-04 |
|
phyclone
|
public |
Accurate Bayesian reconstruction of cancer phylogenies from bulk sequencing.
|
2025-03-04 |
|
pyrodigal
|
public |
Python bindings to Prodigal, an ORF finder for microbial sequences.
|
2025-03-04 |
|
fgbio-minimal
|
public |
A set of tools for working with genomic and high throughput sequencing data, including UMIs
|
2025-03-04 |
|
mumemto
|
public |
Finding maximal unique matches across pangenomes
|
2025-03-03 |
|
panaroo
|
public |
panaroo - an updated pipeline for pangenome investigation
|
2025-03-03 |
|
planemo
|
public |
Command-line utilities to assist in building tools for the Galaxy project (http://galaxyproject.org/).
|
2025-03-03 |
|
gofasta
|
public |
Genomic epidemiology utilities for short genome alignments
|
2025-03-03 |
