nf-core / rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
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RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Repository to host tool-specific module files for the Nextflow DSL2 community!
Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.
B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
Please consider using/contributing to https://github.com/nf-core/sarek
CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.
Protein 3D structure prediction pipeline
Analysis of Chromosome Conformation Capture data (Hi-C)
Highly parallelised multi-taxonomic profiling of shotgun metagenomic data
Genome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed annotation.
ChIP-seq peak-calling, QC and differential analysis pipeline.
k-mer similarity analysis pipeline
Pipeline for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.
De novo assembly pipeline for 10X linked-reads using Supernova
DEPRECIATED! Please use nf-core/tools instead
Nanopore demultiplexing, QC and alignment pipeline
An analysis pipeline for Nanostring nCounter expression data.
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
Assembly and intrahost / low-frequency variant calling for viral samples
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
A small-RNA sequencing analysis pipeline
(Meta-)genome screening for functional and natural product gene sequences
Pipeline for processing spatially-resolved gene counts with spatial coordinates, image data, and optionally single cell RNA-seq data, designed for 10x genomics visium and single cell transcriptomics.