pheniqsFast and accurate sequence demultiplexing
Stars: ✭ 14 (-65.85%)
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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QuagmirA python-based isomiR quantification and analysis pipeline
Stars: ✭ 9 (-78.05%)
gencoreGenerate duplex/single consensus reads to reduce sequencing noises and remove duplications
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GatkOfficial code repository for GATK versions 4 and up
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RoaryRapid large-scale prokaryote pan genome analysis
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Mosdepthfast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
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indigoIndigo: SNV and InDel Discovery in Chromatogram traces obtained from Sanger sequencing of PCR products
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AribaAntimicrobial Resistance Identification By Assembly
Stars: ✭ 96 (+134.15%)
pblatparallelized blat with multi-threads support
Stars: ✭ 34 (-17.07%)
FluentDNAFluentDNA allows you to browse sequence data of any size using a zooming visualization similar to Google Maps. You can use FluentDNA as a standalone program or as a python module for your own bioinformatics projects.
Stars: ✭ 52 (+26.83%)
GubbinsRapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
Stars: ✭ 67 (+63.41%)
ShastaDe novo assembly from Oxford Nanopore reads.
Stars: ✭ 188 (+358.54%)
FastpAn ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
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HMMRATACHMMRATAC peak caller for ATAC-seq data
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GalaxyData intensive science for everyone.
Stars: ✭ 812 (+1880.49%)
AfterqcAutomatic Filtering, Trimming, Error Removing and Quality Control for fastq data
Stars: ✭ 169 (+312.2%)
gff3toemblConverts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
Stars: ✭ 27 (-34.15%)
UgeneUGENE is free open-source cross-platform bioinformatics software
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saffrontreeSaffronTree: Reference free rapid phylogenetic tree construction from raw read data
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IsobarA Python library for creating and manipulating musical patterns, designed for use in algorithmic composition, generative music and sonification. Can be used to generate MIDI events, MIDI files, OSC messages, or custom events.
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Beet.jsPolyrhythmic Sequencer library for Web Audio API.
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astarixAStarix: Fast and Optimal Sequence-to-Graph Aligner
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desh-dataSequence lineage information extracted from RKI sequence data repo
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Mirdeep2Discovering known and novel miRNAs from small RNA sequencing data
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DeepvariantDeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Stars: ✭ 2,404 (+5763.41%)
SnsAnalysis pipelines for sequencing data
Stars: ✭ 43 (+4.88%)
dynamic-discrete-choiceMatlab package for learning to specify, compute, and estimate dynamic discrete choice models
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MigmapHTS-compatible wrapper for IgBlast V-(D)-J mapping tool
Stars: ✭ 38 (-7.32%)
SnapatacAnalysis Pipeline for Single Cell ATAC-seq
Stars: ✭ 183 (+346.34%)
snp-sitesFinds SNP sites from a multi-FASTA alignment file
Stars: ✭ 182 (+343.9%)
Helmsmanhighly-efficient & lightweight mutation signature matrix aggregation
Stars: ✭ 19 (-53.66%)
Rnaseq WorkflowA repository for setting up a RNAseq workflow
Stars: ✭ 170 (+314.63%)
FetchSimple & Efficient data access for Scala and Scala.js
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HLAxHLA: Fast and accurate HLA typing from short read sequence data
Stars: ✭ 84 (+104.88%)
HgvsPython library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
Stars: ✭ 138 (+236.59%)
covid-19-signalFiles and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.
Stars: ✭ 31 (-24.39%)
RNASeqRNASeq pipeline
Stars: ✭ 30 (-26.83%)
ANCOMBCDifferential abundance (DA) and correlation analyses for microbial absolute abundance data
Stars: ✭ 60 (+46.34%)
fastq utilsValidation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.
Stars: ✭ 25 (-39.02%)
CirclatorA tool to circularize genome assemblies
Stars: ✭ 121 (+195.12%)
plasmidtronAssembling the cause of phenotypes and genotypes from NGS data
Stars: ✭ 27 (-34.15%)
HtsjdkA Java API for high-throughput sequencing data (HTS) formats.
Stars: ✭ 220 (+436.59%)
catchA package for designing compact and comprehensive capture probe sets.
Stars: ✭ 55 (+34.15%)
GenomicsA collection of scripts and notes related to genomics and bioinformatics
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InSilicoSeq🚀 A sequencing simulator
Stars: ✭ 116 (+182.93%)
tracyBasecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files
Stars: ✭ 73 (+78.05%)
ATACseqAnalysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
Stars: ✭ 51 (+24.39%)
GenomicsqliteGenomics Extension for SQLite
Stars: ✭ 90 (+119.51%)
bxtoolsTools for analyzing 10X Genomics data
Stars: ✭ 39 (-4.88%)
OttoSampler, Sequencer, Multi-engine synth and effects - in a box! [WIP]
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TruvariStructural variant toolkit for VCFs
Stars: ✭ 85 (+107.32%)
SpringFASTQ compression
Stars: ✭ 71 (+73.17%)
gubbinsRapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
Stars: ✭ 103 (+151.22%)
cacaoCallable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer
Stars: ✭ 21 (-48.78%)
SequenceserverIntuitive local web frontend for the BLAST bioinformatics tool
Stars: ✭ 198 (+382.93%)
Fastq.bioAn interactive web tool for quality control of DNA sequencing data
Stars: ✭ 76 (+85.37%)