Topic: sequencing Goto Github

👇 Here are 450 public repositories matching this topic...

ablab / spades
sequencing,SPAdes Genome Assembler
Organization: ablab
Home Page: http://ablab.github.io/spades/
genome-assembly illumina metagenome-assembly next-generation-sequencing sequence-assembler sequencing transcriptome-assembly

acenglish / truvari
sequencing,Structural variant toolkit for VCFs
User: acenglish
structural-variation vcf bioinformatics data-science genomics vcf-comparison annotation-tool sv-merging benchmarking sequencing

biocommons / hgvs
sequencing,Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
Organization: biocommons
Home Page: https://hgvs.readthedocs.io/
bioinformatics genomics sequencing genome-analysis variant-analysis variation

bitfieldaudio / otto
sequencing,Sampler, Sequencer, Multi-engine synth and effects - in a box! [WIP]
Organization: bitfieldaudio
Home Page: https://bitfieldaudio.com
audio raspberry-pi ui-design synthesizer synth audio-processing music sequencing

brentp / mosdepth
sequencing,fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
User: brentp
coverage genome depth exome wgs sequencing nim nim-lang hacktoberfest

broadinstitute / gatk
sequencing,Official code repository for GATK versions 4 and up
Organization: broadinstitute
Home Page: https://software.broadinstitute.org/gatk
genomics spark science dna ngs sequencing genome bioinformatics gatk

cbg-ethz / v-pipe
sequencing,V-pipe is a pipeline designed for analysing NGS data of short viral genomes
Organization: cbg-ethz
Home Page: https://cbg-ethz.github.io/V-pipe/
ngs snakemake conda biohackeu20 virus sequencing bioinformatics bioinformatics-pipeline biohackcovid20 sars-cov-2

chanzuckerberg / shasta
sequencing,[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads
Organization: chanzuckerberg
dna sequencing assembly nanopore pacbio long-read de-novo

galaxyproject / galaxy
sequencing,Data intensive science for everyone.
Organization: galaxyproject
Home Page: https://galaxyproject.org
bioinformatics workflow genomics science sequencing ngs dna usegalaxy pipeline workflow-engine

gear-genomics / tracy
sequencing,Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files
Organization: gear-genomics
Home Page: https://www.gear-genomics.com/
chromatogram pcr tracy sanger-trace-alignment sanger-sequencing sequencing variant-calling alignment genetic-engineering pcr-products

google / best
sequencing,Bam Error Stats Tool (best): analysis of error types in aligned reads.
Organization: google
bioinformatics sequencing

google / deepvariant
sequencing,DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Organization: google
tensorflow deep-neural-network genomics science dna sequencing genome bioinformatics deep-learning ngs

hadrieng / insilicoseq
sequencing,:rocket: A sequencing simulator
User: hadrieng
Home Page: https://insilicoseq.readthedocs.io
bioinformatics illumina-sequencing sequencing simulation metagenomics

ideoforms / isobar
sequencing,A 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.
User: ideoforms
Home Page: http://ideoforms.github.io/isobar/
music composition algorithmic-composition sequencing midi

igordot / genomics
sequencing,A collection of scripts and notes related to genomics and bioinformatics
User: igordot
bioinformatics genomics sequencing illumina fasta fastq gtf vcf nanopore dna

kairosresearchlab / kairos
sequencing,A complete framework for data control and composition in the vvvv visual programming environment.
Organization: kairosresearchlab
animation automation blending composition control-systems data-layer interpolation sequencing timeline vl

liulabub / hmmratac
sequencing,HMMRATAC peak caller for ATAC-seq data
Organization: liulabub
peak-caller atac-seq peak-detection sequencing machine-learning

looselab / readfish
sequencing,CLI tool for flexible and fast adaptive sampling on ONT sequencers
Organization: looselab
Home Page: https://looselab.github.io/readfish/
adaptive-sampling bioinformatics genomics ont oxford-nanopore sequencing

milaboratory / mixcr
sequencing,MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
Organization: milaboratory
Home Page: https://mixcr.com
bioinformatics immunology antibody t-cell-receptor t-cell rep-seq 10x rna-seq sequencing single-cell

mlin / genomicsqlite
sequencing,Genomics Extension for SQLite
User: mlin
bioinformatics genomics sequencing sqlite sqlite3

nextstrain / nextclade
sequencing,Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
Organization: nextstrain
Home Page: https://clades.nextstrain.org
clade clades coronavirus covid covid-19 dna ncov neherlab nextstrain research

nickjcroucher / gubbins
sequencing,Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
User: nickjcroucher
Home Page: http://nickjcroucher.github.io/gubbins/
bioinformatics bioinformatics-pipeline genomics global-health infectious-diseases next-generation-sequencing pathogen research sequencing

opengene / afterqc
sequencing,Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
Organization: opengene
quality-control fastq ngs sequencing bioinformatics overlap trimming filtering error qc

opengene / fastp
sequencing,An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
Organization: opengene
fastq qc preprocessing filtering adapter overlap quality trimming splitting quality-control

opengene / fastv
sequencing,An ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. This tool can be used to detect viral infectious diseases, like COVID-19.
Organization: opengene
covid-19 sars-cov-2 hcov 2019-ncov sequencing bioinformatics ngs mngs coronavirus covid

opengene / gencore
sequencing,Generate duplex/single consensus reads to reduce sequencing noises and remove duplications
Organization: opengene
sequencing ngs bioinformatics sequencing-error consensus deep-sequencing sequencing-noise duplication duplex deduplication

r3fang / snapatac
sequencing,Analysis Pipeline for Single Cell ATAC-seq
User: r3fang
single-cell-atac-seq single-cell-analysis bioinformatics-pipeline epigenetics machine-learning-algorithms sequencing

rajewsky-lab / mirdeep2
sequencing,Discovering known and novel miRNAs from small RNA sequencing data
Organization: rajewsky-lab
mirna microrna smallrna sequencing analysis prediction quantification mapping

robertaboukhalil / fastq.bio
sequencing,An interactive web tool for quality control of DNA sequencing data
User: robertaboukhalil
Home Page: https://fastq.bio
bioinformatics genomics sequencing fastqc webassembly wasm

samtools / htsjdk
sequencing,A Java API for high-throughput sequencing data (HTS) formats.
Organization: samtools
Home Page: http://samtools.github.io/htsjdk/
genomics sequencing dna ngs bam cram sam fasta vcf java-api

sanger-pathogens / ariba
sequencing,Antimicrobial Resistance Identification By Assembly
Organization: sanger-pathogens
Home Page: http://sanger-pathogens.github.io/ariba/
genomics sequencing next-generation-sequencing research bioinformatics bioinformatics-pipeline global-health infectious-diseases pathogen

sanger-pathogens / artemis
sequencing,Artemis 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
Organization: sanger-pathogens
Home Page: http://sanger-pathogens.github.io/Artemis
genomics sequencing next-generation-sequencing research bioinformatics bioinformatics-pipeline global-health infectious-diseases pathogen

sanger-pathogens / assembly-stats
sequencing,Get assembly statistics from FASTA and FASTQ files
Organization: sanger-pathogens
genomics sequencing next-generation-sequencing research bioinformatics global-health infectious-diseases pathogen

sanger-pathogens / circlator
sequencing,A tool to circularize genome assemblies
Organization: sanger-pathogens
Home Page: http://sanger-pathogens.github.io/circlator/
genomics sequencing next-generation-sequencing research bioinformatics bioinformatics-pipeline global-health infectious-diseases pathogen

sanger-pathogens / roary
sequencing,Rapid large-scale prokaryote pan genome analysis
Organization: sanger-pathogens
Home Page: http://sanger-pathogens.github.io/Roary
genomics sequencing next-generation-sequencing research bioinformatics bioinformatics-pipeline global-health infectious-diseases pathogen

sanger-pathogens / snp-sites
sequencing,Finds SNP sites from a multi-FASTA alignment file
Organization: sanger-pathogens
Home Page: http://sanger-pathogens.github.io/snp-sites/
genomics sequencing next-generation-sequencing research bioinformatics bioinformatics-pipeline global-health infectious-diseases pathogen

shubhamchandak94 / spring
sequencing,FASTQ compression
User: shubhamchandak94
fastq-files compression illumina-binning fastq-compression sequencing

sortmerna / sortmerna
sequencing,SortMeRNA: next-generation sequence filtering and alignment tool
Organization: sortmerna
Home Page: https://sortmerna.readthedocs.io
cpp python alignment bioinformatics metatranscriptomics ngs sequencing

telatin / seqfu2
sequencing,:rocket: seqfu - Sequece Fastx Utilities
User: telatin
Home Page: https://telatin.github.io/seqfu2
fastq fasta bioinformatics bioinformatics-tool bioconda genomics ngs sequencing

tmhglnd / mercury
sequencing,A minimal and human-readable language and environment for the live coding of algorithmic electronic music.
User: tmhglnd
Home Page: http://www.timohoogland.com/mercury-livecoding
mercury mercury-environment human-readable-language language visuals sounds livecoding live-coding performance creative-coding

tobiasrausch / alfred
sequencing,BAM Statistics, Feature Counting and Annotation
User: tobiasrausch
Home Page: https://www.gear-genomics.com/alfred/
insert-size coverage-distribution sequencing quality read-counts quality-control alfred alignment-metrics feature-counting

tobiasrausch / wally
sequencing,Wally: Visualization of aligned sequencing reads and contigs
User: tobiasrausch
genomics sequencing visualization alignment sequencing-data mapping plotting assembly contigs

twbattaglia / rnaseq-workflow
sequencing,A repository for setting up a RNAseq workflow
User: twbattaglia
bioinformatics rna-seq workflow pipeline genes sequencing science

ugeneunipro / ugene
sequencing,UGENE is free open-source cross-platform bioinformatics software
Organization: ugeneunipro
Home Page: http://ugene.net
ugene bioinformatics ngs dna workflow pipeline science cpp qt5 sequencing

verisimilitudex / dnanalyzer
sequencing,Revolutionizing DNA analysis and making it accessible to all through innovative AI-powered analysis and interpretive tools
User: verisimilitudex
Home Page: http://www.dnanalyzer.org/
amino-acid-sequence artificial-intelligence bioinformatics dna dna-sequencing genomics hacktoberfest machine-learning metagenomics protein-sequences regulatory-elements sequencing transcriptomics

wurmlab / sequenceserver
sequencing,Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)
Organization: wurmlab
Home Page: https://sequenceserver.com
blast bioinformatics sequencing genomics-visualization genomics visualization sequence-alignment hacktoberfest ruby javascript

xebia-functional / fetch
sequencing,Simple & Efficient data access for Scala and Scala.js
Organization: xebia-functional
Home Page: https://xebia-functional.github.io/fetch/
scala scala-js cats monix data data-fetching parallelism concurrency sequencing monads

yaqiangcao / cloops
sequencing,Accurate and flexible loops calling tool for 3D genomic data.
User: yaqiangcao
Home Page: https://yaqiangcao.github.io/cLoops/
bioinformatics chia-pet hichip chromatin-interaction 3d-genome hi-c clustering dbscan python ngs

zjufanlab / sccatch
sequencing,Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
User: zjufanlab
Home Page: https://www.sciencedirect.com/science/article/pii/S2589004220300663
marker-genes cell-markers cluster-annotation seurat single-cell rna-seq transcriptomics sequencing transcriptome

zya / beet.js
sequencing,Polyrhythmic Sequencer library for Web Audio API.
User: zya
Home Page: http://zya.github.io/beet.js
webaudio webaudio-api library sequencing audio music js