atropos
An NGS read trimming tool that is specific, sensitive, and speedy. (production)
pysam
Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.
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`).
spilterlize_integrate
A Snakemake workflow and MrBiomics module to split, filter, normalize, integrate and select highly variable features of count matrices resulting from next-generation sequencing (NGS) experiments (e.g., RNA-seq, ATAC-seq, ChIP-seq, Methyl-seq, miRNA-seq,...) including confounding factor analysis and diagnostic visualizations.
https://github.com/cbg-ethz/cowwid
Procedure used for the surveillance of SARS-CoV-2, RSV and Influenza genomic variants in wastewater.
cb-platon
Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
circrna
circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data
svist4get
A simple visualisation tool for genomic tracks from sequencing experiments.
https://github.com/broadinstitute/gatk
Official code repository for GATK versions 4 and up
https://github.com/cokelaer/damona
singularity environment manager (application to NGS and bioinformatics)
https://github.com/cbg-ethz/v-pipe
V-pipe is a pipeline designed for analysing NGS data of short viral genomes
rnftools
RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.
crispresso
Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data
microhapdb
Portable database of microhaplotype marker and allele frequency data
circle-map
A method for circular DNA detection based on probabilistic mapping of ultrashort reads
grabseqs
A utility for easy downloading of reads from next-gen sequencing repositories like NCBI SRA
tophat-recondition
Post-processor for TopHat unmapped.bam files making them usable by downstream software.
https://github.com/ampliconsuite/ampliconreconstructorom
Reconstructs complex variation using Bionano optical mapping data and breakpoint graph data
hicup-plus
Hi-C data processing pipeline (with Dragen, HiSAT2, or STAR aligner)
replitimer
Step-by-step instructions and Snakemake pipeline for processing Replication Timing Data
sammyseq
Pipeline for Sequential Analysis of MacroMolecules accessibilitY sequencing (SAMMY-seq) data, to analyze chromatin state.
germline-structuralv-nf
Germline structural variant calling pipeline for short read WGS datasets
smallvariants
A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data
atacseq_pipeline
Ultimate ATAC-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.
xpresspipe
An alignment and analysis pipeline for Ribosome Profiling and RNA-seq data
ngs-ig
A pipeline for preprocessing and annotation of NGS immunoglobulin repertoire data.
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.
hmnfusion
A tool to aggregate results of fusion produced by Genefuse and Lumpy and calculate allelic frequency
fetch_ngs
Workflow to Fetch Public Sequencing Data and Metadata Using iSeq and MrBiomics Module.
rnaseq_pipeline
RNA-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.
ngs-variants-training
GitHub for the SIB courses NGS - Genome variant analysis
viralmetagenome
Detect iSNV and construct whole viral genomes from metagenomic samples
ngs-preprocess
A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies