stupornova33/MiSiPi.RNA

Characterization of small RNA pathways

Language: R - Size: 4.12 MB - Last synced: about 1 hour ago - Pushed: about 3 hours ago - Stars: 1 - Forks: 0

deeptools/deepTools

Tools to process and analyze deep sequencing data.

Language: Python - Size: 118 MB - Last synced: 26 days ago - Pushed: about 1 month ago - Stars: 645 - Forks: 205

samtools/htslib

C library for high-throughput sequencing data formats

Language: C - Size: 12.4 MB - Last synced: about 2 hours ago - Pushed: 1 day ago - Stars: 775 - Forks: 446

broadinstitute/gatk

Official code repository for GATK versions 4 and up

Language: Java - Size: 453 MB - Last synced: about 5 hours ago - Pushed: about 20 hours ago - Stars: 1,607 - Forks: 574

PavlidisLab/rnaseq-pipeline

RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.

Language: Python - Size: 43.5 MB - Last synced: about 19 hours ago - Pushed: about 20 hours ago - Stars: 19 - Forks: 4

ablab/IsoQuant

Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)

Language: Python - Size: 18.7 MB - Last synced: about 18 hours ago - Pushed: about 21 hours ago - Stars: 119 - Forks: 11

bioforensics/MicroHapulator

Tools for empirical microhaplotype calling, forensic interpretation, and simulation.

Language: Python - Size: 11.2 MB - Last synced: about 21 hours ago - Pushed: 2 days ago - Stars: 6 - Forks: 1

nf-core/hgtseq

A pipeline to investigate horizontal gene transfer from NGS data

Language: Nextflow - Size: 5.11 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 18 - Forks: 4

bodeolukolu/GBSapp

Automated Pipeline for Variant/Haplotype Calling and Filtering

Language: Shell - Size: 2.96 GB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 7 - Forks: 1

IARCbioinfo/IARC-nf

List of IARC bioinformatics nextflow pipelines

Size: 389 KB - Last synced: about 9 hours ago - Pushed: 1 day ago - Stars: 43 - Forks: 10

google/deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Language: Python - Size: 503 MB - Last synced: 1 day ago - Pushed: about 2 months ago - Stars: 3,084 - Forks: 695

OpenGene/fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

Language: C++ - Size: 728 KB - Last synced: 1 day ago - Pushed: about 1 month ago - Stars: 1,779 - Forks: 330

SlowSD/Tutorial-Next-Generation-Sequence-Analysis

This repository summarizes complete NGS analysis for a beginner.

Size: 1.65 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 0 - Forks: 0

YichaoOU/HemTools

HemTools: a collection of NGS pipelines and bioinformatic analyses

Language: Python - Size: 844 MB - Last synced: about 22 hours ago - Pushed: 2 days ago - Stars: 59 - Forks: 16

ngless-toolkit/ngless

NGLess: NGS with less work

Language: Haskell - Size: 14.2 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 143 - Forks: 25

stajichlab/PHYling

Unified PHYling pipeline for species tree building from annotated genomes (see https://github.com/stajichlab/AAFTF and https://github.com/nextgenusfs/funannotate for assembly and annotation steps)

Language: Python - Size: 13.2 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 5 - Forks: 3

mattgalbraith/BaSH_seq

This pipeline processes high-throughput sequencing data (PE/SE) through QC,trim/filter,alignment,counting etc via sequential stages, with individual samples run in parallel via submission to a Slurm queue.

Language: Shell - Size: 131 KB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 1 - Forks: 0

samtools/htsjdk

A Java API for high-throughput sequencing data (HTS) formats.

Language: Java - Size: 109 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 272 - Forks: 244

galaxyproject/galaxy

Data intensive science for everyone.

Language: Python - Size: 616 MB - Last synced: 15 days ago - Pushed: 15 days ago - Stars: 1,315 - Forks: 961

jodyphelan/TBProfiler

Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data

Language: Python - Size: 8.62 MB - Last synced: about 10 hours ago - Pushed: about 11 hours ago - Stars: 88 - Forks: 40

LOVDnl/LOVDplus

LOVD+ -- LOVD for diagnostics: analysis of whole-exome data using LOVD.

Language: PHP - Size: 27.9 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 4 - Forks: 1

ShuXingYu94/NGS_Process_Sample

Language: Shell - Size: 121 KB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 2 - Forks: 0

bialimed/MInITI

Detecting microsatellites instability by high throughput sequencing.

Language: HTML - Size: 13.8 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 0 - Forks: 0

alipirani88/snpkit

Modular workflow for Microbial Variant Calling and SNP diagnostics.

Language: Python - Size: 61.8 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 4 - Forks: 4

lgmgeo/AnnotSV

Annotation and Ranking of Structural Variation

Language: Tcl - Size: 85.2 MB - Last synced: 3 days ago - Pushed: 4 days ago - Stars: 192 - Forks: 36

nf-cmgg/structural

A bioinformatics best-practice analysis pipeline for calling structural variants (SVs), copy number variants (CNVs) and repeat region expansions (RREs) from short DNA reads

Language: Nextflow - Size: 5.62 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 5 - Forks: 3

lpryszcz/bin

My bioinfo toolbox

Language: Python - Size: 81.8 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 47 - Forks: 31

fmalmeida/ngs-preprocess

A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies

Language: Nextflow - Size: 5.31 MB - Last synced: about 10 hours ago - Pushed: about 12 hours ago - Stars: 28 - Forks: 4

nsbuitrago/vfind

Simple variant finding from NGS data

Language: Rust - Size: 46.9 KB - Last synced: 4 days ago - Pushed: 5 days ago - Stars: 1 - Forks: 1

harrlol/hamrbox

A bundle of HAMRtools for High-throughput RNA modification prediction and analysis

Language: R - Size: 111 KB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 0 - Forks: 1

renatosantos98/GLIMPSE-low-coverage-WGS-imputation

Supporting data for "Low-coverage whole genome sequencing for a highly selective cohort of severe COVID-19 patients"

Language: Python - Size: 28.7 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 2 - Forks: 0

BU-ISCIII/iskylims

is an open-source LIMS (laboratory Information Management System) for Next Generation Sequencing sample management, statistics and reports, and bioinformatics analysis service management.

Language: Python - Size: 22.4 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 62 - Forks: 29

stjude-rust-labs/wdl

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

Language: Rust - Size: 387 KB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 14 - Forks: 4

xiaoli-dong/pathogenseq

Pathogen whole genome sequence (WGS) data analysis pipeline

Language: Nextflow - Size: 2.47 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 2 - Forks: 1

wheretrue/exon

Exon is an OLAP query engine specifically for biology and life science applications.

Language: Rust - Size: 55.8 MB - Last synced: 9 days ago - Pushed: 10 days ago - Stars: 27 - Forks: 1

SamuelNicaise/variantconvert

A customizable genetic variants file format converter.

Language: Python - Size: 6.55 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 9 - Forks: 2

YogiOnBioinformatics/The-Epigenetic-Landscape-of-PTSD

Lecture given in University of Pittsburgh course Genomics (BIOSC 1250) related to the epigenetic-basis for PTSD, how methylation of cytosines is detected and how epigenetic modifications of PTSD are hereditary.

Size: 12.3 MB - Last synced: 9 days ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

YogiOnBioinformatics/Maternal-to-Zygotic-Transition-in-Xenopus-laevis

Research project undertaken in Computational Genomics at the University of Pittsburgh. with Dr. Miler Lee and students to understand Maternal-to-Zygotic transition in Xenopus laevis

Language: Shell - Size: 1.9 MB - Last synced: 9 days ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

YogiOnBioinformatics/Assorted-Computational-Genomics-Data-Visualizations

Biplots, Volcano plots, PCA plots, Heatmaps and more Computational Genomics data created and visualized during University of Pittsburgh course, Computational Biology (BIOSC1540), with Dr. Miler Lee

Language: R - Size: 1.73 MB - Last synced: 9 days ago - Pushed: over 5 years ago - Stars: 1 - Forks: 1

y9c/cutseq

✂️ Trim sequencing adapters from NGS data automatically

Language: Python - Size: 2.89 MB - Last synced: 8 days ago - Pushed: 9 days ago - Stars: 3 - Forks: 0

whl-usc/cris_tools

A collection of various tools useful for the deep analysis of data generated via the CRSSANT/rna2d3d pipeline.

Language: Python - Size: 1.22 MB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 1 - Forks: 0

fulcrumgenomics/fgbio

Tools for working with genomic and high throughput sequencing data.

Language: Scala - Size: 9.09 MB - Last synced: 8 days ago - Pushed: 10 days ago - Stars: 304 - Forks: 68

baku4/sigalign

A Similarity-Guided Alignment Algorithm

Language: Rust - Size: 18.7 MB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 10 - Forks: 1

telatin/seqfu2

:rocket: seqfu - Sequece Fastx Utilities

Language: Nim - Size: 78 MB - Last synced: 1 day ago - Pushed: 24 days ago - Stars: 102 - Forks: 6

jdidion/atropos

An NGS read trimming tool that is specific, sensitive, and speedy. (production)

Language: Python - Size: 327 MB - Last synced: 2 days ago - Pushed: 5 months ago - Stars: 118 - Forks: 14

epigen/atacseq_pipeline

Ultimate ATAC-seq Data Processing & Quantification Workflow. A Snakemake implementation of the BSF's ATAC-seq Data Processing Pipeline extended by downstream quantification and annotation steps using bash and Python.

Language: Python - Size: 46.4 MB - Last synced: 10 days ago - Pushed: 11 days ago - Stars: 27 - Forks: 2

nf-cmgg/germline

A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data

Language: Nextflow - Size: 8.53 MB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 4 - Forks: 1

cpwardell/FiNGS

Filters for Next Generation Sequencing

Language: Python - Size: 4.31 MB - Last synced: 7 days ago - Pushed: almost 2 years ago - Stars: 9 - Forks: 0

YU-Zhejian/art_modern

A modernized ART for Illumina read simulation.

Language: C++ - Size: 1.79 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 0 - Forks: 0

esohkevin/esohkevin.github.io

esohinformatics

Size: 25.1 MB - Last synced: 13 days ago - Pushed: 14 days ago - Stars: 0 - Forks: 0

open2c/pairtools

flexible suite of CLI tools for contact extraction (.pairs) from sequencing data (Hi-C, Micro-C and other chromosome capture methods)

Language: Python - Size: 3.25 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 87 - Forks: 35

lindenb/jvarkit

Java utilities for Bioinformatics

Language: Java - Size: 58.9 MB - Last synced: 14 days ago - Pushed: 14 days ago - Stars: 467 - Forks: 129

jlanga/smsk_popoolation

Snakemake pipeline for Popoolation and Popoolation2

Language: Perl - Size: 16.1 MB - Last synced: 13 days ago - Pushed: 14 days ago - Stars: 5 - Forks: 2

bioforensics/MicroHapDB

Portable database of microhaplotype marker and allele frequency data

Language: Python - Size: 450 MB - Last synced: 14 days ago - Pushed: 5 months ago - Stars: 8 - Forks: 3

pughlab/ped_CapTCRseq

Dynamics of peripheral T-cell repertoire in pediatric cancer patients over the course of chemoradiation

Language: Jupyter Notebook - Size: 53.6 MB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 1 - Forks: 0

UPHL-BioNGS/Grandeur

UPHL's Reference Free Pipeline

Language: Nextflow - Size: 512 MB - Last synced: 15 days ago - Pushed: 15 days ago - Stars: 21 - Forks: 6

sii-companion/companion

A genome annotation tool for more than just protists

Language: Lua - Size: 28.3 MB - Last synced: 16 days ago - Pushed: 16 days ago - Stars: 4 - Forks: 3

sebastian-gregoricchio/Rseb

An R-package for daily tasks required to handle biological data as well as avoid re-coding of small functions for quick but necessary data management.

Language: R - Size: 12.9 MB - Last synced: 16 days ago - Pushed: 16 days ago - Stars: 0 - Forks: 1

aidenlab/juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

Language: Shell - Size: 77.3 MB - Last synced: 14 days ago - Pushed: 3 months ago - Stars: 390 - Forks: 180

solida-core/solida

SOLIDA is command-line solution that facilitate the reproducibility and portability of NGS pipelines. It can easily organize the deployment, the data management and the execution of a Snakemake based workflow.

Language: Python - Size: 126 KB - Last synced: 17 days ago - Pushed: about 2 months ago - Stars: 4 - Forks: 1

bpucker/MGSE

Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.

Language: Python - Size: 245 KB - Last synced: 17 days ago - Pushed: 17 days ago - Stars: 28 - Forks: 3

cbg-ethz/V-pipe

V-pipe is a pipeline designed for analysing NGS data of short viral genomes

Language: Jupyter Notebook - Size: 14.7 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 125 - Forks: 41

mazzalab/fastqwiper

An ensamble method to recover corrupted FASTQ files, drop or fix pesky lines, remove unpaired reads, and fix reads interleaving.

Language: Python - Size: 578 KB - Last synced: 8 days ago - Pushed: 6 months ago - Stars: 16 - Forks: 1

tobiasrausch/vc

A tutorial on structural variant calling for short read sequencing data

Language: R - Size: 96.7 KB - Last synced: 20 days ago - Pushed: 21 days ago - Stars: 14 - Forks: 1

KatharineME/FASTQ.jl

DNA and cDNA sequence analysis

Language: Julia - Size: 72.4 MB - Last synced: 9 days ago - Pushed: 21 days ago - Stars: 6 - Forks: 0

open2c/cooler

A cool place to store your Hi-C

Language: Python - Size: 88.1 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 189 - Forks: 53

CVUA-RRW/FooDMe

A reproducible and scalable snakemake workflow for the analysis of DNA metabarcoding experiments, with a special focus on food and feed samples.

Language: Python - Size: 3.88 MB - Last synced: 21 days ago - Pushed: 21 days ago - Stars: 3 - Forks: 1

indexofire/pathongs

Pathogen NGS Documentary

Size: 16.8 MB - Last synced: 25 days ago - Pushed: 25 days ago - Stars: 119 - Forks: 87

sequana/rnaseq

RNA-seq, QC and differential analysis pipeline

Language: R - Size: 3.03 MB - Last synced: 16 days ago - Pushed: 3 months ago - Stars: 17 - Forks: 4

qbicsoftware-archive/variantcalling

Repository for variant calling pipeline using FreeBayes

Language: Python - Size: 5.86 KB - Last synced: 23 days ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

qbicsoftware-archive/variant-annotation-workflow

Workflow scripts of the variant annotation workflow

Language: Python - Size: 1.95 KB - Last synced: 23 days ago - Pushed: about 6 years ago - Stars: 1 - Forks: 0

qbicsoftware-archive/somatic-variantcalling-workflow

Workflow scripts for somatic variant calling workflow (Strelka)

Language: Python - Size: 1000 Bytes - Last synced: 23 days ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

qbicsoftware-archive/rnamapping

RNAseq workflow

Language: Python - Size: 26.4 KB - Last synced: 23 days ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 0

qbicsoftware-archive/qbic-workflow-indproteome

Workflow to create personalized protein references using FRED2.

Language: Python - Size: 14.6 KB - Last synced: 23 days ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 0

qbicsoftware-archive/qbic-workflow-epitopeprediction

Epitope prediction workflow based on FRED.

Language: Python - Size: 2.93 KB - Last synced: 23 days ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

qbicsoftware-archive/optitype-workflow

Language: Python - Size: 18.6 KB - Last synced: 23 days ago - Pushed: over 6 years ago - Stars: 1 - Forks: 0

qbicsoftware-archive/ngsqc

Quality Control on fastq files

Language: Python - Size: 4.88 KB - Last synced: 23 days ago - Pushed: over 8 years ago - Stars: 0 - Forks: 0

qbicsoftware-archive/merge-NGSdata-workflow

Workflow scripts for merging NGS raw data (lanes)

Language: Python - Size: 1000 Bytes - Last synced: 23 days ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

qbicsoftware-archive/epaa-workflow

Language: Python - Size: 24.4 KB - Last synced: 23 days ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 0

qbicsoftware-archive/differentialexpression-analysis-workflow

Differential expression analysis using DESeq2

Language: R - Size: 6.84 KB - Last synced: 23 days ago - Pushed: about 6 years ago - Stars: 1 - Forks: 0

garcia-nacho/TOP

Bacterial swiss-army-knife pipeline for NGS data

Language: Python - Size: 25.3 MB - Last synced: 23 days ago - Pushed: 23 days ago - Stars: 0 - Forks: 0

zavolanlab/htsinfer

Infer metadata for your downstream analysis straight from your RNA-seq data

Language: Python - Size: 6.72 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 8 - Forks: 22

viromelab/tracespipe

Reconstruction and analysis of viral and host genomes at multi-organ level

Language: Shell - Size: 14.9 MB - Last synced: 24 days ago - Pushed: 24 days ago - Stars: 17 - Forks: 6

lifematics/aptamCORE

GUI application for aptamer enrichment analysis

Language: JavaScript - Size: 9.21 MB - Last synced: 24 days ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

sequana/sequana

Sequana: a set of Snakemake NGS pipelines

Language: Jupyter Notebook - Size: 35.5 MB - Last synced: 21 days ago - Pushed: about 2 months ago - Stars: 140 - Forks: 27

Sydney-Informatics-Hub/Germline-StructuralV-nf

Germline structural variant calling pipeline for short read WGS datasets

Language: Nextflow - Size: 1.18 MB - Last synced: 25 days ago - Pushed: about 1 month ago - Stars: 2 - Forks: 3

Sydney-Informatics-Hub/bamQC-nf

Report summary statistics relating to quality of bam files with Nextflow

Language: Nextflow - Size: 1.03 MB - Last synced: 25 days ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

indexofire/pangs

Pathogen NGS Documents

Language: HTML - Size: 789 KB - Last synced: 25 days ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

ugeneunipro/ugene

UGENE is free open-source cross-platform bioinformatics software

Language: C++ - Size: 194 MB - Last synced: 27 days ago - Pushed: 28 days ago - Stars: 196 - Forks: 59

gaarangoa/genomic-scripts

This repository contains simple scripts for genomics/metagenomics data analysis

Language: Python - Size: 601 KB - Last synced: 25 days ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 0

Joon-Klaps/viralgenie

Detect iSNV and construct whole viral genomes from metagenomic samples

Language: Nextflow - Size: 53.9 MB - Last synced: 26 days ago - Pushed: 27 days ago - Stars: 7 - Forks: 1

guigolab/grape-nf

An automated RNA-seq pipeline using Nextflow

Language: Nextflow - Size: 5.43 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 35 - Forks: 10

nf-core/circrna

circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data

Language: Nextflow - Size: 61.8 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 37 - Forks: 17

sortmerna/sortmerna

SortMeRNA: next-generation sequence filtering and alignment tool

Language: C++ - Size: 88.9 MB - Last synced: 26 days ago - Pushed: 27 days ago - Stars: 224 - Forks: 68

maxplanck-ie/snakepipes

Customizable workflows based on snakemake and python for the analysis of NGS data

Language: Python - Size: 39.7 MB - Last synced: 28 days ago - Pushed: 28 days ago - Stars: 369 - Forks: 85

epam/cloud-pipeline

Cloud agnostic genomics analysis, scientific computation and storage platform

Language: Java - Size: 165 MB - Last synced: 27 days ago - Pushed: 28 days ago - Stars: 142 - Forks: 59

ShujiaHuang/basevar

This is the official development repository for BaseVar, which call variants for large-scale ultra low-pass (<1.0x) WGS data, especially for NIPT data

Language: Python - Size: 42.2 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 20 - Forks: 7

galaxyproject/training-material

A collection of Galaxy-related training material

Language: HTML - Size: 10.4 GB - Last synced: 27 days ago - Pushed: 27 days ago - Stars: 293 - Forks: 838

nf-core/crisprseq

A pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted next generation sequencing (NGS) data (`targeted`) as well as the discovery of important genes from knock-out or activation CRISPR-Cas9 screens using CRISPR pooled DNA (`screening`).

Language: Nextflow - Size: 6.84 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 21 - Forks: 19

oicr-gsi/miso-lims Fork of miso-lims/miso-lims 📦

MISO: An open-source LIMS for NGS sequencing centres, now with detailed samples

Language: Ruby - Size: 164 MB - Last synced: 26 days ago - Pushed: over 3 years ago - Stars: 10 - Forks: 6