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Bioconda Recipes ⭐ 1,488

Conda recipes for the bioconda channel.

Multiqc ⭐ 1,015

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

Sniffles ⭐ 363

Structural variation caller using third generation sequencing

Cellrank ⭐ 236

CellRank for directed single-cell fate mapping

Bioconvert ⭐ 236

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

Survivor ⭐ 193

Toolset for SV simulation, comparison and filtering

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

NGLess: NGS with less work

Instrain ⭐ 97

Bioinformatics program inStrain

Pyrodigal ⭐ 90

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

Run_dbcan ⭐ 86

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

🚀 seqfu - Sequece Fastx Utilities

Characterization of Germline variants

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

Bioinformatics in Python

Deep Learning based cell composition analysis with Scaden.

HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

Peptide Shaker ⭐ 37

Interpretation of proteomics identification results

Covtobed ⭐ 36

⛰ covtobed | Convert the coverage track from a BAM file into a BED file

Bioconda.github.io ⭐ 31

Bioconda is a distribution of bioinformatics software realized as a channel for the versatile package manager Conda.

Searchgui ⭐ 30

Highly adaptable common interface for proteomics search and de novo engines

A python package and a set of shell commands to handle GTF files

Ribocode ⭐ 28

release version

Ploidy agnostic phasing pipeline and algorithm

Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.

SINA - Reference based multiple sequence alignment

Plasmidtron ⭐ 16

Assembling the cause of phenotypes and genotypes from NGS data

Towards fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics.

🐳 Dugong - Scientific Linux Container

Mlst_check ⭐ 14

Multilocus sequence typing by blast using the schemes from PubMLST

A robust model for quantitative comparison of ChIP-Seq data sets.

Flexible omics pipeline

Scaffold_builder ⭐ 12

Combining de novo and reference-guided assembly with Scaffold_builder

Bio Tradis ⭐ 12

A set of tools to analyse the output from TraDIS analyses

Set of tools for viral metagenomics.

Containers Rules Manuscript ⭐ 10

Recommendations to contenarized your bioinformatics software

Library for indexing VCF files for random access searches by rsID

Ng Meta Profiler ⭐ 10

Profiler for metagenomics based on NGLess

Schicexplorer ⭐ 8

Single-cell Hi-C data analysis toolbox

🎉 CNVetti – robust, efficient, and versatile clinical CNV calling from HTS data

Visualize HMMs, CMs and their comparisons

Bioconda Tutorial ⭐ 5

A quick overview of how to use Bioconda, and create recipes

FOCUS: An Agile Profiler for Metagenomic Data

Build A Reproducible Jupyter Workflow From Scratch ⭐ 3

Build a Reproducible Jupyter Workflow From Scratch (2017 NIH Hour of Code)

Qiime2 Artifact eXtractor

PyPairs - A python scRNA-Seq classifier

Cubi_demux ⭐ 3

Demultiplexing utility, companion to flowcelltool.

Dugongbioinformatics.github.io ⭐ 3

🐳 Dugong Project Website

Bioinfo Notebook ⭐ 2

🔬 Bioinformatics Notebook. Scripts for bioinformatics pipelines, with quick start guides for programs and video demonstrations.

Dugonggui ⭐ 2

🐳 Dugong - Scientific Linux Container

Wp2_workshop_tool_packaging ⭐ 2

Workshops ⭐ 2

Repository for BioContainers Hackthons and Workshops

Milestone ⭐ 1

bacterial strain identification

Perl Biotool ⭐ 1

🐫 🐪 Small pure Perl5 libraries for writing command line bioinformatics tools

Azolla_genus_metagenome ⭐ 1

This project aims do describe and explore the metagenomes of fern species of the genus Azolla.

Bioconda Mpi ⭐ 1

Docker container for developing bioinformatics applications in Python using Jupyter notebook

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