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NextflowA DSL for data-driven computational pipelines
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UgeneUGENE is free open-source cross-platform bioinformatics software
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DecontamSimple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
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BlacklistApplication for making ENCODE Blacklists
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IndraINDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.
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AribaAntimicrobial Resistance Identification By Assembly
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Fastq.bioAn interactive web tool for quality control of DNA sequencing data
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FqtoolsAn efficient FASTQ manipulation suite
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FastqtFastQC port to Qt5: A quality control tool for high throughput sequence data.
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ScgenSingle cell perturbation prediction
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SwarmA robust and fast clustering method for amplicon-based studies
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ClusterflowA pipelining tool to automate and standardise bioinformatics analyses on cluster environments.
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SarekDetect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing
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TruvariStructural variant toolkit for VCFs
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TaxonkitA Practical and Efficient NCBI Taxonomy Toolkit
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Dna2vecdna2vec: Consistent vector representations of variable-length k-mers
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Biosequences.jlBiological sequences for the julia language
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GenomicsA collection of scripts and notes related to genomics and bioinformatics
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PlipProtein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Salentin et al. (2015), https://www.doi.org/10.1093/nar/gkv315
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BioconvertBioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.
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CirclatorA tool to circularize genome assemblies
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PyaniPython module for average nucleotide identity analyses
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VdjtoolsPost-analysis of immune repertoire sequencing data
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Bioconda RecipesConda recipes for the bioconda channel.
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HicexplorerHiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
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SortmernaSortMeRNA: next-generation sequence filtering and alignment tool
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GoenrichGO enrichment with python -- pandas meets networkx
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DeepecgECG classification programs based on ML/DL methods
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BedtkA simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
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SplatterSimple simulation of single-cell RNA sequencing data
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Somalierfast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
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Krakenuniq🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results
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