nf-core pipeline · archived · chip-ssds, dmc1-ssds, dsbs
nf-core/ssds
Processes single-stranded DNA sequencing data to map single-stranded DNA and double-strand break sites.
What nf-core/ssds is
nf-core/ssds is a bioinformatics analysis pipeline designed for processing Single-Stranded DNA Sequencing (SSDS) assays. Originally authored by Kevin Brick with contributions from Flor Pratto, it provides a standardised workflow for mapping and analysing genomic single-stranded DNA.
The pipeline addresses the requirement to distinguish single-stranded DNA signatures from double-stranded backgrounds in genomic studies, including meiotic double-strand breaks and DNA replication origins. It processes raw sequencing data, separates single-stranded and double-stranded alignments, and outputs enrichment calculations alongside normalised genomic coverage tracks.
Implemented in Nextflow DSL2 using containerised processes, the pipeline has been archived and is no longer actively maintained.
What the pipeline does
Raw sequencing reads first undergo quality control using FastQC and adapter and quality trimming using Trim Galore. The trimmed reads are aligned to the reference genome with BWA MEM, after which the resulting alignments are sorted using Picard and indexed using Samtools.
Specialised SSDS accessory scripts parse the BAM file to separate single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) fractions and calculate enrichment metrics. Coverage tracks are constructed using Bedtools and UCSC tools, additional quality metrics are derived with deepTools, and a final summary report is compiled with MultiQC.
Key facts
- Pipeline engine
- Nextflow (DSL2)
- Minimum Nextflow version
- 21.10.3
- Original author
- Kevin Brick
- Contributor
- Flor Pratto
- Status
- Archived (no longer maintained)
- Primary aligner
- BWA MEM
- Supported container engines
- Docker, Singularity, Podman, Shifter, Charliecloud
- QC reporting
- MultiQC
What you can use it for
- Meiotic double-strand break mapping
- Mapping meiotic recombination hotspots and double-strand break sites using DMC1 ChIP-SSDS sequencing data.
- Replication origin identification
- Detecting and profiling DNA replication origins across the genome from ori-SSDS experiments.
- ssDNA and dsDNA separation
- Filtering and categorising aligned sequencing reads into distinct single-stranded and double-stranded DNA fractions.
- SSDS coverage track generation
- Building normalised genomic coverage tracks and calculating region-specific enrichment values from parsed SSDS alignments.
Strengths and limits
Good at
- Separates single-stranded and double-stranded DNA alignments using dedicated parsing tools.
- Implements Nextflow DSL2 with per-process containerisation supporting Docker, Singularity, Podman, Shifter, and Charliecloud.
- Combines FastQC, deepTools, and MultiQC to produce a unified quality assessment across all pipeline stages.
- Provides automated processing from raw reads through to genome coverage tracks and enrichment metrics.
Watch out for
- The repository is archived and is no longer maintained.
- Requires Nextflow version 21.10.3 or higher.
- Relies on external custom accessory scripts for core ssDNA parsing and enrichment calculations.
Questions
Can I run nf-core/ssds without my own cluster?
The research agent runs nf-core/ssds with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
What licence is nf-core/ssds under?
MIT, like every nf-core pipeline.
What sequencing assays can this pipeline analyse?
It is designed for Single-Stranded DNA Sequencing (SSDS) assays, including DMC1 ChIP-SSDS for meiotic double-strand breaks and ori-SSDS for replication origins.
How are ssDNA and dsDNA reads distinguished?
Following alignment with BWA MEM, sorting with Picard, and indexing with Samtools, dedicated SSDS accessory scripts parse the alignments into ssDNA and dsDNA subsets.
Is nf-core/ssds actively maintained?
No, the pipeline has been archived and is no longer actively maintained.
What inputs are required to run an analysis?
The workflow requires a sample sheet in CSV format specifying the input read files and an appropriate reference genome.
How to cite it
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.
Written from nf-core/ssds's own README. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.