UgeneUGENE is free open-source cross-platform bioinformatics software
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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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Somalierfast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
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Apbs Pdb2pqrAPBS - software for biomolecular electrostatics and solvation
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NextflowA DSL for data-driven computational pipelines
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Hts Nimnim wrapper for htslib for parsing genomics data files
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CgrangesA C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)
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SmudgeplotInference of ploidy and heterozygosity structure using whole genome sequencing data
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Krakenuniq🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results
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Dna2vecdna2vec: Consistent vector representations of variable-length k-mers
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BioBioinformatics library for .NET
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MrbayesMrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:
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FqtoolsAn efficient FASTQ manipulation suite
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PysradbPackage for fetching metadata and downloading data from SRA/ENA/GEO
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BiofastBenchmarking programming languages/implementations for common tasks in Bioinformatics
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SplatterSimple simulation of single-cell RNA sequencing data
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TaxonkitA Practical and Efficient NCBI Taxonomy Toolkit
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Soapdenovo2Next generation sequencing reads de novo assembler.
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GenomicsA collection of scripts and notes related to genomics and bioinformatics
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SarekDetect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing
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AribaAntimicrobial Resistance Identification By Assembly
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ArtemisArtemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation
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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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HicexplorerHiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
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OctopusBayesian haplotype-based mutation calling
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NglessNGLess: NGS with less work
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KaijuFast taxonomic classification of metagenomic sequencing reads using a protein reference database
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CoolerA cool place to store your Hi-C
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BiotiteA comprehensive library for computational molecular biology
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Bio4jBio4j abstract model and general entry point to the project
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BiograknBioGrakn Knowledge Graph
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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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ReadfqFast multi-line FASTA/Q reader in several programming languages
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PyaniPython module for average nucleotide identity analyses
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PegasusPegasus Workflow Management System - Automate, recover, and debug scientific computations.
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SortmernaSortMeRNA: next-generation sequence filtering and alignment tool
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BedtkA simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
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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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PymzmlpymzML - an interface between Python and mzML Mass spectrometry Files
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HgvsPython library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
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BionitioDemonstrating best practices for bioinformatics command line tools
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DeepecgECG classification programs based on ML/DL methods
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Dnachisel✏️ A versatile DNA sequence optimizer
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MixcrMiXCR is a universal software for fast and accurate extraction of T- and B- cell receptor repertoires from any type of sequencing data. Free for academic use only.
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Kmer CntCode examples of fast and simple k-mer counters for tutorial purposes
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RiddleRace and ethnicity Imputation from Disease history with Deep LEarning
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HifiasmHifiasm: a haplotype-resolved assembler for accurate Hifi reads
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CirclatorA tool to circularize genome assemblies
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SnprThe sources of the openSNP website
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ClairvoyanteClairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing
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ScdeR package for analyzing single-cell RNA-seq data
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Awesome Single CellCommunity-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
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BlacklistApplication for making ENCODE Blacklists
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