next-generation-sequencing

There are 20 repositories under next-generation-sequencing topic.

ablab / spades
SPAdes Genome Assembler
genome-assembly sequence-assembler sequencing transcriptome-assembly illumina metagenome-assembly next-generation-sequencing
Language:C++ 720
jvarkit
lindenb / jvarkit
Java utilities for Bioinformatics
bioinformatics biology genomics java next-generation-sequencing ngs science
Language:Java 476
openbiox / awosome-bioinformatics
A curated list of resources for learning bioinformatics.
bioinformatics data-analysis next-generation-sequencing
439
nf-core / sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
nextflow workflow pipeline bioinformatics genomics cancer next-generation-sequencing conda reproducible-research containers germline somatic variant-calling nf-core gatk4 annotation whole-genome-sequencing whole-exome-sequencing pre-processing target-panels
Language:Nextflow 354
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 307
philres / ngmlr
NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations
next-generation-sequencing pacbio oxford-nanopore mapper structural-variations long-read alignment bioconda docker
Language:C++ 284
bioinformatics-centre / kaiju
Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
metagenomics next-generation-sequencing bioinformatics taxonomic-classification taxonomy
Language:C 258
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 231
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 231
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 223
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:Rust 206
sanger-pathogens / ariba
Antimicrobial Resistance Identification By Assembly
genomics sequencing next-generation-sequencing research bioinformatics bioinformatics-pipeline global-health infectious-diseases pathogen
Language:Python 167
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 161
ngless-toolkit / ngless
NGLess: NGS with less work
bioinformatics bioinformatics-pipeline bwa fastq fastq-format genomics haskell haskell-language metagenomics next-generation-sequencing ngs samtools science
Language:Haskell 142
alastair-droop / fqtools
An efficient FASTQ manipulation suite
bioinformatics fastq fastq-files next-generation-sequencing
Language:C 134
Sarek
SciLifeLab / Sarek
Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing
nextflow workflow pipeline bioinformatics genomics cancer next-generation-sequencing docker singularity reproducible-science reproducible-research containers germline germline-variants somatic somatic-variants
Language:Nextflow 132
zhanxw / rvtests
Rare variant test software for next generation sequencing data
next-generation-sequencing ngs association-analysis gwas rare-variant meta-analysis genotype skat c-plus-plus variants umich genetics kernel vcf-files
Language:C++ 126
sanger-pathogens / assembly-stats
Get assembly statistics from FASTA and FASTQ files
genomics sequencing next-generation-sequencing research bioinformatics global-health infectious-diseases pathogen
Language:C++ 110
SNPGenie
chasewnelson / SNPGenie
Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
snp-report fasta-sequences next-generation-sequencing dnds-estimation dnds nucleotide diversity-measurement nucleotide-diversity sequence-analysis population-genetics evolution molecular-evolution evolutionary-parameters substitution-rate nei-gojobori natural-selection vcf vcf-files perl
Language:Perl 100
xjtu-omics / msisensor-pro
Microsatellite Instability (MSI) detection using high-throughput sequencing data.
dna-missmatch-repair-system hypermutation microsatellite-instability next-generation-sequencing tumor-only-support
Language:C++ 93
KHP-Informatics / ngseasy
Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)
ngs docker next-generation-sequencing pipeline shell
Language:Shell 86
Cibiv / NextGenMap
NextGenMap is a flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms while still outperforming them in terms of runtime. This allows analysing large scale datasets even with increased SNP rates or higher error rates (e.g. caused by specialized experimental protocols) and avoids biases caused by highly variable regions in the genome.
short-read-mapper next-generation-sequencing c-plus-plus-11 opencl
Language:C++ 85
MicrobeLab / DeepMicrobes
DeepMicrobes: taxonomic classification for metagenomics with deep learning
deep-learning metagenomics next-generation-sequencing bioinformatics microbiome
Language:Python 81
chanzuckerberg / czid-web
Infectious Disease Sequencing Platform
infectious-diseases genomics sequencing metagenomic science next-generation-sequencing research biology virology bioinformatics bioinformatics-pipeline computational-biology global-health czid chan-zuckerberg-id
Language:TypeScript 78
tobiasrausch / ATACseq
Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
atac-seq sequencing chromatin nucleosome-positioning next-generation-sequencing peak-detection atac-seq-pipeline
Language:Shell 73
sanger-pathogens / Fastaq
Python3 scripts to manipulate FASTA and FASTQ files
genomics sequencing next-generation-sequencing research bioinformatics global-health infectious-diseases pathogen
Language:Python 69
stjude-rust-labs / fq
Command line utility for manipulating Illumina-generated FASTQ files.
fastq bioinformatics genomics illumina next-generation-sequencing fastq-files rust
Language:Rust 69
sanger-pathogens / pathogen-informatics-training
genomics sequencing next-generation-sequencing research bioinformatics global-health infectious-diseases pathogen
Language:Jupyter Notebook 65
sanger-pathogens / assembly_improvement
Improve the quality of a denovo assembly by scaffolding and gap filling
genomics sequencing next-generation-sequencing research bioinformatics bioinformatics-pipeline global-health infectious-diseases pathogen
Language:Perl 55
sanger-pathogens / iva
de novo virus assembler of Illumina paired reads
genomics sequencing next-generation-sequencing research bioinformatics bioinformatics-pipeline global-health infectious-diseases pathogen
Language:Python 52
HTStream
s4hts / HTStream
A high throughput sequence read toolset using a streaming approach facilitated by Linux pipes
bioinformatics bioinformatics-tool genomics streaming linux-pipes sequence-analysis next-generation-sequencing
Language:C++ 48
KHP-Informatics / DNAscan
DNAscan is a fast and efficient bioinformatics pipeline that allows for the analysis of DNA Next Generation sequencing data, requiring very little computational effort and memory usage.
ngs next-generation-sequencing pipeline workflow
Language:HTML 43
stjudecloud / oliver
An opinionated Cromwell orchestration manager.
genomics cromwell workflow oliver wdl workflow-execution hpc next-generation-sequencing bioinformatics bioinformatics-pipeline wdl-workflow
Language:Python 40
YaqiangCao / cLoops2
Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.
bioinformatics-tool chromatin-interaction cloops2 clustering loops peaks 3d-genome 3d-genome-visualization domains stripes python chia-pet hi-c trac-looping hichip differential-enriched-loops un-limited-resolution next-generation-sequencing rehoboam montage
Language:Python 40
mehrdadbakhtiari / adVNTR
A tool for genotyping Variable Number Tandem Repeats (VNTR) from sequence data
structural-variation genomics bioinformatics genotype next-generation-sequencing
Language:Python 39
nextgenusfs / amptk
AMPtk: Amplicon ToolKit for NGS data (formally UFITS)
amplicons microbiome mycobiome next-generation-sequencing fungi rdna coi lsu co1 mtco1
Language:Python 35