Bioconda Open Source Projects

Conda recipes for the bioconda channel.

Aggregate results from bioinformatics analyses across many samples into a single report.

Phylogenetic orthology inference for comparative genomics

Structural variation caller using third generation sequencing

A flexible pipeline for complete analysis of bacterial genomes

MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis

CellRank: dynamics from multi-view single-cell data

Toolset for SV simulation, comparison and filtering

Repository to host tool-specific module files for the Nextflow DSL2 community!

Fit data to many distributions

genes and genomes at your fingertips

Read alignment statistics for metagenomics

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

Rapid large-scale prokaryote pan genome analysis

Python package with helper tools for the nf-core community.

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations

PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.

diploid SNV caller for error-prone reads

A set of command line utilities based on Rust-Bio.

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

Bioinformatics program inStrain

Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!

DAS Tool

Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.

BAM Statistics, Feature Counting and Annotation

Convert between AnnData and SingleCellExperiment

Fast HLA type inference from whole-genome data

Assorted tools for interacting with .gct, .gctx files and other Connectivity Map (Broad Institute) data/tools

Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See full GimmeMotifs documentation for detailed installation instructions and usage examples.

:rocket: seqfu - Sequece Fastx Utilities

Ongoing analysis of COVID-19 using Galaxy, BioConda and public research infrastructures

Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files

A Python-based EGA download client

Antibiotic resistance prediction in minutes

main repo: https://github.com/ucscGenomeBrowser/cellBrowser/ - Python pipeline and Javascript scatter plot library for single-cell datasets, http://cellbrowser.rtfd.org

Single-Cell Clustering Assessment Framework

Utilities for building and managing bioconda recipes

Characterization of Germline variants