sequencing

There are 47 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 3092
bitfieldaudio / OTTO
Sampler, Sequencer, Multi-engine synth and effects - in a box! [WIP]
audio raspberry-pi ui-design synthesizer synth audio-processing music sequencing
Language:C++ 2624
OpenGene / fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
adapter bioinformatics duplication fastq filter filtering illumina merging ngs overlap polyg preprocessing qc quality quality-control sequencing splitting trimming umi
Language:C++ 1786
broadinstitute / gatk
Official code repository for GATK versions 4 and up
genomics spark science dna ngs sequencing genome bioinformatics gatk
Language:Java 1613
galaxyproject / galaxy
Data intensive science for everyone.
bioinformatics workflow genomics science sequencing ngs dna usegalaxy pipeline workflow-engine hacktoberfest
Language:Python 1320
ablab / spades
SPAdes Genome Assembler
genome-assembly sequence-assembler sequencing transcriptome-assembly illumina metagenome-assembly next-generation-sequencing
Language:C++ 677
hemberg-lab / scRNA.seq.course
Analysis of single cell RNA-seq data course
bookdown course r scrna-seq scrna-seq-analysis sequencing
Language:TeX 666
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 660
xebia-functional / fetch
Simple & Efficient data access for Scala and Scala.js
cats concurrency data data-fetching monads monix parallelism scala scala-js sequencing
Language:Scala 494
twbattaglia / RNAseq-workflow
A repository for setting up a RNAseq workflow
bioinformatics genes pipeline rna-seq science sequencing workflow
Language:R 382
ideoforms / isobar
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.
music composition algorithmic-composition sequencing midi
Language:Python 357
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 312
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 296
r3fang / SnapATAC
Analysis Pipeline for Single Cell ATAC-seq
single-cell-atac-seq single-cell-analysis bioinformatics-pipeline epigenetics machine-learning-algorithms sequencing
Language:R 295
truvari
ACEnglish / truvari
Structural variant toolkit for VCFs
structural-variation vcf bioinformatics data-science genomics vcf-comparison annotation-tool sv-merging benchmarking sequencing
Language:Python 294
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 274
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 273
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++ 270
wurmlab / sequenceserver
Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)
blast bioinformatics sequencing genomics-visualization genomics visualization sequence-alignment hacktoberfest ruby javascript
Language:JavaScript 266
biocommons / hgvs
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
bioinformatics genomics sequencing genome-analysis variant-analysis variation
Language:Python 232
sortmerna / sortmerna
SortMeRNA: next-generation sequence filtering and alignment tool
cpp python alignment bioinformatics metatranscriptomics ngs sequencing
Language:C++ 229
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 227
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 227
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 218
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 204
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 201
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++ 201
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 200
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 189
HadrienG / InSilicoSeq
:rocket: A sequencing simulator
bioinformatics illumina-sequencing sequencing simulation metagenomics
Language:Python 173
LooseLab / readfish
CLI tool for flexible and fast adaptive sampling on ONT sequencers
adaptive-sampling bioinformatics genomics ont oxford-nanopore sequencing
Language:Python 161
sanger-pathogens / ariba
Antimicrobial Resistance Identification By Assembly
genomics sequencing next-generation-sequencing research bioinformatics bioinformatics-pipeline global-health infectious-diseases pathogen
Language:Python 155
mlin / GenomicSQLite
Genomics Extension for SQLite
sqlite sqlite3 bioinformatics genomics sequencing
Language:C++ 154
nickjcroucher / gubbins
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
genomics sequencing next-generation-sequencing research bioinformatics bioinformatics-pipeline global-health infectious-diseases pathogen
Language:Python 154
tobiasrausch / alfred
BAM Statistics, Feature Counting and Annotation
alfred alignment-metrics coverage-distribution feature-counting insert-size quality quality-control read-counts sequencing
Language:C++ 134
rajewsky-lab / mirdeep2
Discovering known and novel miRNAs from small RNA sequencing data
mirna microrna smallrna sequencing analysis prediction quantification mapping
Language:Perl 129