Helmsmanhighly-efficient & lightweight mutation signature matrix aggregation
Stars: ✭ 19 (-77.65%)
GenomicsA collection of scripts and notes related to genomics and bioinformatics
Stars: ✭ 101 (+18.82%)
MigmapHTS-compatible wrapper for IgBlast V-(D)-J mapping tool
Stars: ✭ 38 (-55.29%)
AfterqcAutomatic Filtering, Trimming, Error Removing and Quality Control for fastq data
Stars: ✭ 169 (+98.82%)
RoaryRapid large-scale prokaryote pan genome analysis
Stars: ✭ 176 (+107.06%)
SvtyperBayesian genotyper for structural variants
Stars: ✭ 79 (-7.06%)
Fastq.bioAn interactive web tool for quality control of DNA sequencing data
Stars: ✭ 76 (-10.59%)
UgeneUGENE is free open-source cross-platform bioinformatics software
Stars: ✭ 112 (+31.76%)
CirclatorA tool to circularize genome assemblies
Stars: ✭ 121 (+42.35%)
SVCollectorMethod to optimally select samples for validation and resequencing
Stars: ✭ 20 (-76.47%)
Vcfannoannotate a VCF with other VCFs/BEDs/tabixed files
Stars: ✭ 259 (+204.71%)
GatkOfficial code repository for GATK versions 4 and up
Stars: ✭ 1,002 (+1078.82%)
HailScalable genomic data analysis.
Stars: ✭ 706 (+730.59%)
Hap.pyHaplotype VCF comparison tools
Stars: ✭ 249 (+192.94%)
TypeTEGenotyping of segregating mobile elements insertions
Stars: ✭ 15 (-82.35%)
SnsAnalysis pipelines for sequencing data
Stars: ✭ 43 (-49.41%)
AribaAntimicrobial Resistance Identification By Assembly
Stars: ✭ 96 (+12.94%)
BiosyntaxSyntax highlighting for computational biology
Stars: ✭ 164 (+92.94%)
saffrontreeSaffronTree: Reference free rapid phylogenetic tree construction from raw read data
Stars: ✭ 17 (-80%)
catchA package for designing compact and comprehensive capture probe sets.
Stars: ✭ 55 (-35.29%)
gff3toemblConverts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
Stars: ✭ 27 (-68.24%)
plasmidtronAssembling the cause of phenotypes and genotypes from NGS data
Stars: ✭ 27 (-68.24%)
GalaxyData intensive science for everyone.
Stars: ✭ 812 (+855.29%)
GubbinsRapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
Stars: ✭ 67 (-21.18%)
Tiledb VcfEfficient variant-call data storage and retrieval library using the TileDB storage library.
Stars: ✭ 26 (-69.41%)
Rnaseq WorkflowA repository for setting up a RNAseq workflow
Stars: ✭ 170 (+100%)
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
Stars: ✭ 135 (+58.82%)
Cyvcf2cython + htslib == fast VCF and BCF processing
Stars: ✭ 243 (+185.88%)
HgvsPython library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
Stars: ✭ 138 (+62.35%)
gencoreGenerate duplex/single consensus reads to reduce sequencing noises and remove duplications
Stars: ✭ 91 (+7.06%)
SequenceserverIntuitive local web frontend for the BLAST bioinformatics tool
Stars: ✭ 198 (+132.94%)
DeepvariantDeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Stars: ✭ 2,404 (+2728.24%)
HtsjdkA Java API for high-throughput sequencing data (HTS) formats.
Stars: ✭ 220 (+158.82%)
HtslibC library for high-throughput sequencing data formats
Stars: ✭ 529 (+522.35%)
SurvivorToolset for SV simulation, comparison and filtering
Stars: ✭ 180 (+111.76%)
PygenoPersonalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
Stars: ✭ 261 (+207.06%)
16gtSimultaneous detection of SNPs and Indels using a 16-genotype probabilistic model
Stars: ✭ 26 (-69.41%)
FastpAn ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
Stars: ✭ 966 (+1036.47%)
LambdaLAMBDA – the Local Aligner for Massive Biological DatA
Stars: ✭ 59 (-30.59%)
FlowrRobust and efficient workflows using a simple language agnostic approach
Stars: ✭ 73 (-14.12%)
Qiime16stutorialA tutorial on methods of 16S analysis with QIIME 1
Stars: ✭ 59 (-30.59%)
Dna NnModel and predict short DNA sequence features with neural networks
Stars: ✭ 59 (-30.59%)
StartappThe START App: R Shiny Transcriptome Analysis Resource Tool
Stars: ✭ 73 (-14.12%)
DynverseA set of tools supporting the development, execution, and benchmarking of trajectory inference methods. 🌍
Stars: ✭ 58 (-31.76%)
Pairix1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates
Stars: ✭ 57 (-32.94%)
BgtFlexible genotype query among 30,000+ samples whole-genome
Stars: ✭ 72 (-15.29%)
Cwl SvgA library for generating an interactive SVG visualization of CWL workflows
Stars: ✭ 57 (-32.94%)
PhpbenchPHP Benchmarking framework
Stars: ✭ 1,235 (+1352.94%)
Mygene.infoMyGene.info: A BioThings API for gene annotations
Stars: ✭ 79 (-7.06%)
Coursera SpecializationsSolutions to assignments of Coursera Specializations - Deep learning, Machine learning, Algorithms & Data Structures, Image Processing and Python For Everybody
Stars: ✭ 72 (-15.29%)
Pytest Django QueriesGenerate performance reports from your django database performance tests.
Stars: ✭ 54 (-36.47%)
Jsperf.comjsperf.com v2. https://github.com/h5bp/lazyweb-requests/issues/174
Stars: ✭ 1,178 (+1285.88%)
GenozipCompressor for genomic files (FASTQ, SAM/BAM, VCF, FASTA, GVF, 23andMe...), up to 5x better than gzip and faster too
Stars: ✭ 53 (-37.65%)
Sv2Support Vector Structural Variation Genotyper
Stars: ✭ 52 (-38.82%)
Biosequences.jlBiological sequences for the julia language
Stars: ✭ 77 (-9.41%)
Awesome Expression Browser😎 A curated list of software and resources for exploring and visualizing (browsing) expression data 😎
Stars: ✭ 72 (-15.29%)