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An open API service indexing awesome lists of open source software.

Projects in Awesome Lists tagged with next-generation-sequencing

A curated list of projects in awesome lists tagged with next-generation-sequencing .

https://github.com/openbiox/awosome-bioinformatics

A curated list of resources for learning bioinformatics.

bioinformatics data-analysis next-generation-sequencing

Last synced: 08 Jan 2026

https://github.com/nf-core/sarek

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

annotation bioinformatics cancer conda containers gatk4 genomics germline next-generation-sequencing nextflow nf-core pipeline pre-processing reproducible-research somatic target-panels variant-calling whole-exome-sequencing whole-genome-sequencing workflow

Last synced: 12 Feb 2026

https://github.com/bioinformatics-centre/kaiju

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

bioinformatics metagenomics next-generation-sequencing taxonomic-classification taxonomy

Last synced: 21 Feb 2026

https://github.com/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

alignment bioconda docker long-read mapper next-generation-sequencing oxford-nanopore pacbio structural-variations

Last synced: 14 Apr 2025

https://github.com/nextstrain/nextclade

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

clade clades coronavirus covid covid-19 covid19 dna influenza ncov neherlab next-generation-sequencing nextstrain research rna sars-cov-2 science sequences sequencing strain virus

Last synced: 15 Apr 2026

https://github.com/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

Last synced: 01 Apr 2026

https://github.com/stjude-rust-labs/fq

Command line utility for manipulating Illumina-generated FASTQ files.

bioinformatics fastq fastq-files genomics illumina next-generation-sequencing rust

Last synced: 21 Oct 2025

https://github.com/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.

c-plus-plus-11 next-generation-sequencing opencl short-read-mapper

Last synced: 19 Apr 2025

https://github.com/tobiasrausch/atacseq

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

atac-seq atac-seq-pipeline chromatin next-generation-sequencing nucleosome-positioning peak-detection sequencing

Last synced: 18 Mar 2026

https://github.com/zhanxw/seqminer

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

annotation bcf bgen meta-analysis next-generation-sequencing plink sequencing tabix vcf workflow

Last synced: 18 Feb 2026

https://github.com/TimoLassmann/samstat

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

bioinformatics next-generation-sequencing quality-control

Last synced: 05 May 2025

https://github.com/genometric/mspc

Using combined evidence from replicates to evaluate ChIP-seq peaks

analysis chip-seq enriched-regions genome-analysis mspc next-generation-sequencing ngs-analysis overlapping-peaks peak peaks

Last synced: 12 Apr 2025

https://github.com/futianfan/genocraft

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

bulk-rna-seq flask genomics multiomics next-generation-sequencing ngs omics omics-data-integration pathway-analysis protein rna-seq single-cell visualization

Last synced: 12 Oct 2025

https://github.com/epigen/fetch_ngs

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

bam database fastq genomics next-generation-sequencing ngs repository

Last synced: 14 Sep 2025

https://github.com/stjudecloud/ngsderive

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

bioinformatics computational-biology gene-model genomics next-generation-sequencing ngs strandedness strandedness-inference workflow workflow-engine

Last synced: 11 Jul 2025

https://github.com/fls-bioinformatics-core/auto_process_ngs

Scripts and utilities for automatic processing & management of Illumina NGS sequencing data within the Bioinformatics Core Facility at the University of Manchester

10xgenomics automation bioinformatics fastq-files illumina next-generation-sequencing pipeline qc sequencing

Last synced: 23 Jan 2026

https://github.com/bihealth/cnvetti

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

bioinformatics copy-number-variation next-generation-sequencing

Last synced: 12 Feb 2026

https://github.com/kohyamat/massgenotyping

Python package for microsatellite genotyping from highly multiplexed amplicon sequencing data

amplicon-sequencing genotyping microsatellite next-generation-sequencing

Last synced: 14 Jan 2026

https://github.com/wpwupingwp/divide

Divide NGS data by barcode and primer

dna-barcode-extraction next-generation-sequencing

Last synced: 17 Jan 2026

https://github.com/dfornika/miseq-samplesheet-parser

Parse illumina MiSeq SampleSheet.csv files and convert to JSON

bioinformatics illumina miseq next-generation-sequencing

Last synced: 20 May 2026

https://github.com/sivkri/small-rna-seq-analysis

scripts and resources for performing miRNA sequencing analysis using tools like mirPRo and miRDeep2. Explore the code to process reads, map them to the genome, quantify known miRNAs, identify novel miRNAs, and browse the results

bioinformatics gene-expression-analysis mirna mirna-seq mirna-sequencing next-generation-sequencing rna-seq-analysis small-rna-analysis

Last synced: 19 May 2026

https://github.com/phac-nml/submitdatairidanext

Pipeline for submitting data to INSDC databases for IRIDA Next

data-sharing data-submission file-transfer microbial-genomics next-generation-sequencing

Last synced: 16 Jan 2026

https://github.com/fullscreen-triangle/gospel

Framework for comprehensive variant detection in whole genome sequences using advanced machine learning models for cross domain pattern recognition in fitness, pharmacogenetics and nutritional aspects of sprint running

exome-sequencing next-generation-sequencing pharmacogenetics variant-analysis variant-calling whole-genome-sequencing

Last synced: 16 Aug 2026

https://github.com/neurogenomics/epiprepare

Preprocessing of epigenomic data from fastq files.

epigenomics next-generation-sequencing preprocessing r r-package

Last synced: 27 Jul 2025

https://github.com/astrabert/rrequested

RREQUESTED: A versatile shellscript tool based on Python scripts to preprocess raw basecalled reads with quality and size filtering and ex-novo demultiplexing

beginner-friendly bioinformatics conda demultiplexing easy-to-use genomics next-generation-sequencing oxford-nanopore

Last synced: 05 Mar 2025

https://github.com/mpusp/snakemake-simple-mapping

A Snakemake workflow for the mapping of reads to reference genomes, minimalistic and simple.

bowtie2 bwa-mem2 genomics mapping next-generation-sequencing snakemake snakemake-workflow star-alignment variant-calling

Last synced: 11 Mar 2026

https://github.com/jcaperella29/bwa_samtools_cwl_flow

a common language workflow , workflow to process Fastq files

bioinformatics cwl-workflow next-generation-sequencing

Last synced: 07 Mar 2026

https://github.com/gmauro/presta

Presta handles sequencing data produced from a large scale NGS Core facility. It leverages a reliable distributed task queue to create a messages-driven automation system. Presta is focused on real-time operations, but supports scheduling as well.

message-queue next-generation-sequencing python python-library

Last synced: 29 Mar 2025

https://github.com/tus-kondolab/iso2gene

Cross-platform C/C++ implementation of the tximport algorithm for gene-level quantification

next-generation-sequencing ngs rna-seq rnaseq tximport windows

Last synced: 08 Jun 2026

https://github.com/scholl-lab/plasmicheck

Detect and quantify plasmid DNA contamination in sequencing data

bioinformatics contamination-detection genomics minimap2 next-generation-sequencing plasmid splicing

Last synced: 18 Feb 2026

https://github.com/bccdc-phl/routine-sequence-qc-collector

Collect outputs from BCCDC-PHL/routine-sequence-qc pipeline for usage by BCCDC-PHL/routine-sequence-qc-site

data-management microbial-genomics next-generation-sequencing quality-control

Last synced: 29 Jan 2026