Introduction

schneebergerlab/scatacseqrecomb is a bioinformatics workflow for processing 10X Genomics single-cell ATAC-seq data to detect recombination events. It uses the nf-core template, but is not part of nf-core itself.

1. Read alignment (Cell Ranger ATAC)
2. Calling reference and alternate allele counts at a set of given heterozygous SNPs (cellsnp-lite)

Usage

Notes If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test, mamba before running the workflow on actual data.

This workflow assumes that the cellranger-atac binary is present in your PATH. It can be obtained here.

First, prepare a samplesheet with your input data that looks as follows:

samplesheet.csv:

sample,fastq_dir
atac_seq_sample_1,/path/to/reads/atac_seq_sample_1

Each row contains a sample ID and a path containing all reads (I1, R1, R2, R3) of a particular sample, following the 10X Genomics naming scheme specified here.

Now, you can run the pipeline using:

nextflow run schneebergerlab/scatacseqrecomb \
   -profile <conda/mamba/biohpc_gen> \
   --input samplesheet.csv \
   --reference_config reference_config.config \
   --reference_name reference_name \
   --fasta genome.fa \
   --gtf gene_annotation.gtf \
   --het_snps het_snps.vcf.gz \
   --outdir <OUTDIR>

For more details regarding usage and output, please see the documentation

Warning: Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

Credits

schneebergerlab/scatacseqrecomb was originally written by Raúl Wijfjes.

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.