sequencing

There are 50 repositories under sequencing topic.

google / deepvariant
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
tensorflow deep-neural-network genomics science dna sequencing genome bioinformatics deep-learning ngs deepvariant machine-learning
Language:Python 3545
bitfieldaudio / OTTO
Sampler, Sequencer, Multi-engine synth and effects - in a box! [WIP]
audio audio-processing music raspberry-pi sequencing synth synthesizer ui-design
Language:C++ 2678
OpenGene / fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
fastq qc preprocessing filtering adapter overlap quality trimming splitting quality-control filter ngs bioinformatics umi sequencing illumina polyg duplication merging
Language:C++ 2213
broadinstitute / gatk
Official code repository for GATK versions 4 and up
genomics spark science dna ngs sequencing genome bioinformatics gatk
Language:Java 1867
galaxyproject / galaxy
Data intensive science for everyone.
bioinformatics dna genomics hacktoberfest ngs pipeline science sequencing usegalaxy workflow workflow-engine
Language:Python 1652
ablab / spades
SPAdes Genome Assembler
genome-assembly illumina metagenome-assembly next-generation-sequencing sequence-assembler sequencing transcriptome-assembly
Language:C++ 874
brentp / mosdepth
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
coverage genome depth exome wgs sequencing nim nim-lang hacktoberfest
Language:Nim 788
hemberg-lab / scRNA.seq.course
Analysis of single cell RNA-seq data course
r scrna-seq scrna-seq-analysis bookdown sequencing course
Language:TeX 676
xebia-functional / fetch
Simple & Efficient data access for Scala and Scala.js
scala scala-js cats monix data data-fetching parallelism concurrency sequencing monads
Language:Scala 494
twbattaglia / RNAseq-workflow
A repository for setting up a RNAseq workflow
bioinformatics rna-seq workflow pipeline genes sequencing science
Language:R 445
ideoforms / isobar
A Python package 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 actions.
music composition algorithmic-composition sequencing midi
Language:Python 408
truvari
ACEnglish / truvari
Structural variant toolkit for VCFs
annotation-tool benchmarking bioinformatics data-science genomics sequencing structural-variation sv-merging vcf vcf-comparison
Language:Python 385
milaboratory / mixcr
MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
bioinformatics immunology antibody t-cell-receptor t-cell rep-seq 10x rna-seq sequencing single-cell
Language:Kotlin 377
sanger-pathogens / Roary
Rapid large-scale prokaryote pan genome analysis
genomics sequencing next-generation-sequencing research bioinformatics bioinformatics-pipeline global-health infectious-diseases pathogen
Language:Perl 356
mercury
tmhglnd / mercury
A minimal and human-readable language and environment for the live coding of algorithmic electronic music.
mercury mercury-environment human-readable-language language visuals sounds livecoding live-coding performance creative-coding osc sequencing algorithmic-composition
Language:Max 347
r3fang / SnapATAC
Analysis Pipeline for Single Cell ATAC-seq
bioinformatics-pipeline epigenetics machine-learning-algorithms sequencing single-cell-analysis single-cell-atac-seq
Language:R 320
samtools / htsjdk
A Java API for high-throughput sequencing data (HTS) formats.
genomics sequencing dna ngs bam cram sam fasta vcf java-api java
Language:Java 290
wurmlab / sequenceserver
Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)
bioinformatics blast genomics genomics-visualization hacktoberfest javascript ruby sequence-alignment sequencing visualization
Language:JavaScript 289
biocommons / hgvs
Python library to parse, format, validate, normalize, and map sequence variants according to HGVS Nomenclature (https://hgvs-nomenclature.org/).
bioinformatics genome-analysis genomics hgvs sequencing transcript variant-analysis variation
Language:Python 282
sortmerna / sortmerna
SortMeRNA: next-generation sequence filtering and alignment tool
cpp python alignment bioinformatics metatranscriptomics ngs sequencing
Language:C++ 277
chanzuckerberg / shasta
[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads
dna sequencing assembly nanopore pacbio long-read de-novo
Language:C++ 274
google / deepsomatic
DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal and tumor-only sequencing data.
bioinformatics deep-learning dna genome genomics machine science sequencing somatic-mutations somatic-variants deepsomatic
269
sanger-pathogens / snp-sites
Finds SNP sites from a multi-FASTA alignment file
genomics sequencing next-generation-sequencing research bioinformatics bioinformatics-pipeline global-health infectious-diseases pathogen
Language:C 268
sanger-pathogens / Artemis
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
genomics sequencing next-generation-sequencing research bioinformatics bioinformatics-pipeline global-health infectious-diseases pathogen
Language:Java 258
sanger-pathogens / circlator
A tool to circularize genome assemblies
genomics sequencing next-generation-sequencing research bioinformatics bioinformatics-pipeline global-health infectious-diseases pathogen
Language:Python 248
nextstrain / nextclade
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
clade clades coronavirus covid covid-19 dna ncov neherlab nextstrain research rna sars-cov-2 science sequences sequencing strain virus covid19 next-generation-sequencing influenza
Language:TypeScript 247
ugene
ugeneunipro / ugene
UGENE is free open-source cross-platform bioinformatics software
ugene bioinformatics ngs dna workflow pipeline science cpp qt5 sequencing cross-platform msa
Language:C++ 247
ZJUFanLab / scCATCH
Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
marker-genes cell-markers cluster-annotation seurat single-cell rna-seq transcriptomics sequencing transcriptome
Language:R 234
genomics
igordot / genomics
A collection of scripts and notes related to genomics and bioinformatics
bioinformatics genomics sequencing illumina fasta fastq gtf vcf nanopore dna science workflow fast5
Language:R 217
OpenGene / AfterQC
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
quality-control fastq ngs sequencing bioinformatics overlap trimming filtering error qc adapter-trimming
Language:Python 212
HadrienG / InSilicoSeq
:rocket: A sequencing simulator
bioinformatics illumina-sequencing sequencing simulation metagenomics
Language:Python 211
nickjcroucher / gubbins
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
bioinformatics bioinformatics-pipeline genomics global-health infectious-diseases next-generation-sequencing pathogen research sequencing
Language:Python 206
readfish
LooseLab / readfish
CLI tool for flexible and fast adaptive sampling on ONT sequencers
adaptive-sampling bioinformatics genomics ont oxford-nanopore sequencing
Language:Python 192
sanger-pathogens / ariba
Antimicrobial Resistance Identification By Assembly
genomics sequencing next-generation-sequencing research bioinformatics bioinformatics-pipeline global-health infectious-diseases pathogen
Language:Python 181
mlin / GenomicSQLite
Genomics Extension for SQLite
bioinformatics genomics sequencing sqlite sqlite3
Language:C++ 167
rajewsky-lab / mirdeep2
Discovering known and novel miRNAs from small RNA sequencing data
mirna microrna smallrna sequencing analysis prediction quantification mapping
Language:Perl 154