next-generation-sequencing | Topic

Topic: "next-generation-sequencing"

ablab/spades

SPAdes Genome Assembler

Language: C++ - Size: 97.6 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 820 - Forks: 149

lindenb/jvarkit

Java utilities for Bioinformatics

Language: Java - Size: 60.6 MB - Last synced at: 13 minutes ago - Pushed at: about 1 hour ago - Stars: 498 - Forks: 133

openbiox/awosome-bioinformatics

A curated list of resources for learning bioinformatics.

Size: 360 KB - Last synced at: 8 days ago - Pushed at: about 3 years ago - Stars: 475 - Forks: 125

nf-core/sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

Language: Nextflow - Size: 102 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 442 - Forks: 443

sanger-pathogens/Roary

Rapid large-scale prokaryote pan genome analysis

Language: Perl - Size: 17.7 MB - Last synced at: about 1 month ago - Pushed at: about 3 years ago - Stars: 340 - Forks: 190

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

Language: C++ - Size: 35.4 MB - Last synced at: about 1 month ago - Pushed at: about 1 year ago - Stars: 297 - Forks: 40

bioinformatics-centre/kaiju

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

Language: C - Size: 906 KB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 278 - Forks: 67

sanger-pathogens/snp-sites

Finds SNP sites from a multi-FASTA alignment file

Language: C - Size: 14.7 MB - Last synced at: about 1 month ago - Pushed at: over 4 years ago - Stars: 257 - Forks: 49

sanger-pathogens/circlator

A tool to circularize genome assemblies

Language: Python - Size: 25.7 MB - Last synced at: 23 days ago - Pushed at: about 1 year ago - Stars: 240 - Forks: 57

nextstrain/nextclade

Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement

Language: Rust - Size: 59.2 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 230 - Forks: 61

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

Language: Java - Size: 153 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 208 - Forks: 73

nickjcroucher/gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

Language: Python - Size: 9.69 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 184 - Forks: 53

sanger-pathogens/ariba

Antimicrobial Resistance Identification By Assembly

Language: Python - Size: 12 MB - Last synced at: about 1 month ago - Pushed at: over 1 year ago - Stars: 173 - Forks: 55

ngless-toolkit/ngless

NGLess: NGS with less work

Language: Haskell - Size: 14.1 MB - Last synced at: about 4 hours ago - Pushed at: about 2 months ago - Stars: 146 - Forks: 25

SciLifeLab/Sarek Fork of nf-core/sarek 📦

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

Language: Nextflow - Size: 43.8 MB - Last synced at: about 2 months ago - Pushed at: over 5 years ago - Stars: 133 - Forks: 7

alastair-droop/fqtools

An efficient FASTQ manipulation suite

Language: C - Size: 2.28 MB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 127 - Forks: 16

zhanxw/rvtests

Rare variant test software for next generation sequencing data

Language: C++ - Size: 32.7 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 120 - Forks: 41

chasewnelson/SNPGenie

Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data

Language: Perl - Size: 876 KB - Last synced at: about 2 months ago - Pushed at: over 1 year ago - Stars: 111 - Forks: 37

xjtu-omics/msisensor-pro

Microsatellite Instability (MSI) detection using high-throughput sequencing data.

Language: C++ - Size: 233 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 107 - Forks: 23

sanger-pathogens/assembly-stats

Get assembly statistics from FASTA and FASTQ files

Language: C++ - Size: 1.02 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 95 - Forks: 22

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.

Language: C++ - Size: 113 MB - Last synced at: 25 days ago - Pushed at: almost 6 years ago - Stars: 87 - Forks: 8

chanzuckerberg/czid-web

Infectious Disease Sequencing Platform

Language: TypeScript - Size: 466 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 84 - Forks: 25

KHP-Informatics/ngseasy

Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)

Language: Shell - Size: 44 MB - Last synced at: over 1 year ago - Pushed at: almost 8 years ago - Stars: 84 - Forks: 40

stjude-rust-labs/fq

Command line utility for manipulating Illumina-generated FASTQ files.

Language: Rust - Size: 563 KB - Last synced at: 2 months ago - Pushed at: 3 months ago - Stars: 82 - Forks: 5

tobiasrausch/ATACseq

Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)

Language: Shell - Size: 330 KB - Last synced at: about 1 month ago - Pushed at: almost 2 years ago - Stars: 75 - Forks: 36

MicrobeLab/DeepMicrobes

DeepMicrobes: taxonomic classification for metagenomics with deep learning

Language: Python - Size: 1.25 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 74 - Forks: 19

sanger-pathogens/Fastaq

Python3 scripts to manipulate FASTA and FASTQ files

Language: Python - Size: 371 KB - Last synced at: 18 days ago - Pushed at: about 2 months ago - Stars: 70 - Forks: 21

sanger-pathogens/pathogen-informatics-training

Language: Jupyter Notebook - Size: 359 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 58 - Forks: 34

sanger-pathogens/iva

de novo virus assembler of Illumina paired reads

Language: Python - Size: 8.46 MB - Last synced at: 25 days ago - Pushed at: almost 4 years ago - Stars: 55 - Forks: 18

sanger-pathogens/assembly_improvement

Improve the quality of a denovo assembly by scaffolding and gap filling

Language: Perl - Size: 3.03 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 52 - Forks: 21

stjude-rust-labs/wdl

Rust crates for working with Workflow Description Language (WDL) documents.

Language: Rust - Size: 3.83 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 49 - Forks: 34

epigen/MrBiomics

MrBiomics: Modules & Recipes augment Bioinformatics for Multi-Omics Analyses

Language: Python - Size: 10.1 MB - Last synced at: 29 days ago - Pushed at: about 1 month ago - Stars: 49 - Forks: 1

s4hts/HTStream

A high throughput sequence read toolset using a streaming approach facilitated by Linux pipes

Language: C++ - Size: 20.3 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 49 - Forks: 9

YaqiangCao/cLoops2

Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.

Language: Python - Size: 251 MB - Last synced at: about 1 month ago - Pushed at: 2 months ago - Stars: 46 - Forks: 8

mehrdadbakhtiari/adVNTR

A tool for genotyping Variable Number Tandem Repeats (VNTR) from sequence data

Language: Python - Size: 1.42 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 41 - Forks: 15

stjudecloud/oliver 📦

An opinionated Cromwell orchestration manager.

Language: Python - Size: 2.61 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 40 - Forks: 3

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.

Language: HTML - Size: 57.2 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 39 - Forks: 22

nextgenusfs/amptk

AMPtk: Amplicon ToolKit for NGS data (formally UFITS)

Language: Python - Size: 18.3 MB - Last synced at: 2 months ago - Pushed at: over 1 year ago - Stars: 38 - Forks: 14

stjudecloud/workflows

Bioinformatics workflows developed for and used on the St. Jude Cloud project.

Language: WDL - Size: 74.6 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 36 - Forks: 12

stjude-rust-labs/ngs

Command line utility for working with next-generation sequencing files.

Language: Rust - Size: 893 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 34 - Forks: 2

zhanxw/seqminer

Query sequence data (VCF/BCF1/BCF2, Tabix, BGEN, PLINK) in R

Language: C - Size: 7.99 MB - Last synced at: 23 days ago - Pushed at: 7 months ago - Stars: 30 - Forks: 12

kstawiski/OmicSelector

OmicSelector - Environment, docker-based application and R package for biomarker signiture selection (feature selection) & deep learning diagnostic tool development from high-throughput high-throughput omics experiments and other multidimensional datasets. Initially developed for miRNA-seq, RNA-seq and qPCR.

Language: R - Size: 54.5 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 30 - Forks: 3

ncbi/pm4ngs

Project Manager for NGS data analysis

Language: Python - Size: 14 MB - Last synced at: 5 days ago - Pushed at: over 2 years ago - Stars: 30 - Forks: 10

sanger-pathogens/mlst_check

Multilocus sequence typing by blast using the schemes from PubMLST

Language: Perl - Size: 5.23 MB - Last synced at: about 18 hours ago - Pushed at: almost 3 years ago - Stars: 30 - Forks: 15

sanger-pathogens/gff3toembl

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

Language: Python - Size: 2.92 MB - Last synced at: about 17 hours ago - Pushed at: over 6 years ago - Stars: 29 - Forks: 12

sanger-pathogens/plasmidtron

Assembling the cause of phenotypes and genotypes from NGS data

Language: Python - Size: 825 KB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 28 - Forks: 8

menghaowei/ngstools

My own tools code for NGS data analysis (Next Generation Sequencing)

Language: Python - Size: 2.53 MB - Last synced at: over 1 year ago - Pushed at: almost 6 years ago - Stars: 28 - Forks: 9

stjudecloud/wdldoc

Create WDL documentation using Markdown.

Language: Python - Size: 157 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 27 - Forks: 5

baku4/sigalign

A Similarity-Guided Alignment Algorithm

Language: Rust - Size: 11.7 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 26 - Forks: 4

edgardomortiz/Captus

Assembly of Phylogenomic Datasets from High-Throughput Sequencing data

Language: Python - Size: 77.7 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 25 - Forks: 6

sanger-pathogens/saffrontree

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

Language: Python - Size: 1.32 MB - Last synced at: about 18 hours ago - Pushed at: almost 5 years ago - Stars: 25 - Forks: 3

genid/Yleaf

Yleaf software for human Y-chromosomal haplogroup inference from next generation sequencing data

Language: Python - Size: 41.1 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 24 - Forks: 10

TimoLassmann/samstat

SAMStat displays various properties of next-generation sequencing reads stored in SAM/BAM format.

Language: C - Size: 6.67 MB - Last synced at: 10 days ago - Pushed at: almost 2 years ago - Stars: 24 - Forks: 6

amberbiology/py4lifesci

Code repository for the book "Python for the Life Sciences" by Lancaster & Webster

Language: Python - Size: 8.64 MB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 24 - Forks: 15

GarrettJenkinson/informME

An information-theoretic pipeline for methylation analysis of WGBS data

Language: MATLAB - Size: 7.78 MB - Last synced at: over 1 year ago - Pushed at: about 6 years ago - Stars: 24 - Forks: 9

rhshah/iCallSV

A Framework to call Structural Variants from NGS based datasets

Language: Python - Size: 3.12 MB - Last synced at: 10 days ago - Pushed at: over 7 years ago - Stars: 22 - Forks: 10

sigven/cacao

Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer

Language: R - Size: 20.4 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 21 - Forks: 4

Genometric/MSPC

Using combined evidence from replicates to evaluate ChIP-seq peaks

Language: C# - Size: 22.1 MB - Last synced at: 1 day ago - Pushed at: 16 days ago - Stars: 20 - Forks: 10

sanger-pathogens/Bio-Tradis

A set of tools to analyse the output from TraDIS analyses

Language: Perl - Size: 192 MB - Last synced at: 11 months ago - Pushed at: almost 2 years ago - Stars: 20 - Forks: 29

MorrellLAB/sequence_handling Fork of pmorrell/sequence_handling

A series of scripts to automate sequence workflows

Language: Jupyter Notebook - Size: 6.94 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 18 - Forks: 9

sanger-pathogens/seroba

k-mer based Pipeline to identify the Serotype from Illumina NGS reads

Language: Python - Size: 19.4 MB - Last synced at: 9 months ago - Pushed at: almost 2 years ago - Stars: 18 - Forks: 16

chgibb/PHAT

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

Language: TypeScript - Size: 649 MB - Last synced at: 10 days ago - Pushed at: over 2 years ago - Stars: 17 - Forks: 2

galantelab/sandy

A straightforward and complete next-generation sequencing read simulator

Language: Perl - Size: 25.9 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 15 - Forks: 2

PacificBiosciences/minorseq 📦

Minor Variant Calling and Phasing Tools

Size: 1.96 MB - Last synced at: 10 months ago - Pushed at: over 3 years ago - Stars: 15 - Forks: 6

futianfan/GenoCraft

GenoCraft: A Comprehensive, User-Friendly Web Platform for High-Throughput Omics Data Analysis and Visualization (https://arxiv.org/pdf/2312.14249)

Language: SCSS - Size: 69.9 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 14 - Forks: 0

merlyescalona/ngsphy

NGSphy: phylogenomic simulation of next-generation sequencing data

Language: Python - Size: 16.3 MB - Last synced at: 7 months ago - Pushed at: about 7 years ago - Stars: 14 - Forks: 6

ANGSD-wrapper/angsd-wrapper

Utilities for analyzing next generation sequencing data.

Language: Shell - Size: 13.4 MB - Last synced at: almost 2 years ago - Pushed at: about 4 years ago - Stars: 13 - Forks: 4

Sentieon/sentieon-dnascope-ml

Sentieon DNAscope + Machine Learning Model

Language: Shell - Size: 111 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 12 - Forks: 4

stjudecloud/ngsderive

Forensic analysis tool useful in backwards computing information from next-generation sequencing data.

Language: Python - Size: 1.07 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 11 - Forks: 0

Pathogen-Genomics-Cymru/lodestone

Mycobacterial pipeline

Language: Python - Size: 572 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 11 - Forks: 4

maxemil/PhyloMagnet

screening metagenomes for arbitrary lineages, using gene-centric assembly methods and phylogenetics

Language: Nextflow - Size: 2.34 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 11 - Forks: 4

epigen/fetch_ngs

Workflow to Fetch Public Sequencing Data and Metadata Using iSeq and MrBiomics Module.

Language: Python - Size: 46.9 KB - Last synced at: 29 days ago - Pushed at: about 1 month ago - Stars: 10 - Forks: 0

blachlylab/fade

Fragmentase Artifact Detection and Elimination

Language: D - Size: 721 KB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 10 - Forks: 3

MultiQC/example-plugin

A miniature example of a MultiQC plugin.

Language: Python - Size: 43.9 KB - Last synced at: 10 days ago - Pushed at: 3 months ago - Stars: 9 - Forks: 6

galantelab/sideRETRO

A pipeline for detecting Somatic Insertion of DE novo RETROcopies

Language: C - Size: 4.76 MB - Last synced at: about 1 month ago - Pushed at: 6 months ago - Stars: 9 - Forks: 5

HudsonAlpha/rust-msbwt

place for building up a msbwt resource in Rust

Language: Rust - Size: 156 KB - Last synced at: 15 days ago - Pushed at: over 2 years ago - Stars: 9 - Forks: 2

quadram-institute-bioscience/albatradis

Comparative TraDIS analysis

Language: Gnuplot - Size: 19.6 MB - Last synced at: 10 days ago - Pushed at: over 2 years ago - Stars: 9 - Forks: 4

bihealth/cnvetti

:tada: CNVetti – robust, efficient, and versatile clinical CNV calling from HTS data

Language: Rust - Size: 547 KB - Last synced at: about 1 year ago - Pushed at: over 5 years ago - Stars: 8 - Forks: 0

sepro/LSTrAP 📦

Language: Python - Size: 33.4 MB - Last synced at: about 1 year ago - Pushed at: almost 6 years ago - Stars: 8 - Forks: 4

kaizhang/Taiji 📦

This project has been moved to:

Language: Haskell - Size: 3.67 MB - Last synced at: about 2 years ago - Pushed at: about 6 years ago - Stars: 8 - Forks: 3

yanlinlin82/seqpipe

A framework for SEQuencing data analysis PIPElines.

Language: Perl - Size: 5.33 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 7 - Forks: 4

kohyamat/massgenotyping

Python package for microsatellite genotyping from highly multiplexed amplicon sequencing data

Language: Python - Size: 420 KB - Last synced at: 9 months ago - Pushed at: over 1 year ago - Stars: 7 - Forks: 1

linnil1/HLA_collections

A script to run HLA typing tools from next generation sequencing data

Language: Python - Size: 292 KB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 7 - Forks: 1

stjudecloud/docs-archive 📦

Documentation on St. Jude Cloud.

Language: Shell - Size: 413 MB - Last synced at: 4 months ago - Pushed at: about 3 years ago - Stars: 7 - Forks: 6

stjude/Episomizer

Constuct Extrachromosomal Circular DNA using Whole Genome Sequencing Data

Language: Python - Size: 73.6 MB - Last synced at: about 1 year ago - Pushed at: over 6 years ago - Stars: 7 - Forks: 5

BBCG/epialleleR

Fast, epiallele-aware methylation caller and reporter — an R/Bioconductor package

Language: R - Size: 82.7 MB - Last synced at: 16 days ago - Pushed at: 2 months ago - Stars: 6 - Forks: 1

Roco-scientist/NGS-Barcode-Count

Counts barcodes within next generation sequencing data. DNA encoded libraries (DEL), CRISPR, and barcode-seq

Language: Rust - Size: 346 KB - Last synced at: 13 days ago - Pushed at: over 1 year ago - Stars: 6 - Forks: 4

ucladx/pancan-panel-design

A pan-cancer DNA-seq panel

Language: Python - Size: 3.31 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 6 - Forks: 0

blachlylab/dhtslib

D bindings and OOP wrappers for htslib

Language: D - Size: 1.21 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 6 - Forks: 1

xjtu-omics/Mako

A graph-based pattern growth approach for CSV discovery

Language: Java - Size: 18 MB - Last synced at: about 2 years ago - Pushed at: almost 4 years ago - Stars: 6 - Forks: 1

rcs333/CLOMP

:horse: CLinically Okay Metagenomic Pipeline :horse:

Language: Python - Size: 311 KB - Last synced at: about 1 year ago - Pushed at: over 5 years ago - Stars: 6 - Forks: 3

WCSCourses/NGS_Bioinformatics_2024 Fork of WCSCourses/NGS_Bioinformatics 📦

Learn to analyse next generation sequence data to address a wide range of biological questions

Language: TeX - Size: 137 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 5 - Forks: 2