nf-core pipeline · 3d-genome, chromatin, dna
nf-core/sammyseq
Processes SAMMY-seq sequencing data to investigate chromatin accessibility states and genome compartmentalisation.
What nf-core/sammyseq is
nf-core/sammyseq is a bioinformatics pipeline designed to process Sequential Analysis of MacroMolecules accessibilitY sequencing (SAMMY-seq) data. The method profiles biochemical fractions to study chromatin state and nuclear organisation. The underlying analytical approach was devised by the laboratories of Francesco Ferrari (IFOM-ETS and IGM-CNR) and Chiara Lanzuolo (INGM and ITB-CNR), originally running as a bash workflow on Sun Grid Engine. It is being implemented as an nf-core pipeline by Lucio Di Filippo, Ugo Maria Iannacchero, Nadia Sanseverino, and Margherita Mutarelli.
The pipeline automates read quality assessment, alignment, deduplication, signal track generation, and downstream chromatin compartmentalisation. By standardising these steps, it enables researchers to examine chromatin domains, compare solubility fractions, and evaluate changes in genome compartmentalisation across biological conditions.
What the pipeline does
The analysis begins with sequencing read quality control using FastQC, followed by adapter and low-quality base removal with Trim Galore! or Trimmomatic. Reads are then aligned to a user-provided reference genome using BWA or Bowtie 2. Picard MarkDuplicates marks duplicated reads, and samtools filters the alignments and compiles mapping statistics. deepTools bamCoverage is then employed to build single-track coverage profiles in bigWig format.
Downstream optional analyses include chromosome-wide A/B chromatin compartmentalisation using CALDER2, generation of pairwise comparison tracks in bigWig format via SPP or deepTools bigwigCompare, and detection of differentially enriched solubility regions. Finally, MultiQC aggregates all processing statistics and quality metrics into a single summary report.
Key facts
- Pipeline engine
- Nextflow (nf-core)
- Input formats
- FASTQ (single-end or paired-end), FASTA (reference genome), CSV (samplesheet)
- Output formats
- bigWig, MultiQC HTML report
- Aligners supported
- BWA, Bowtie 2
- Trimming software
- Trim Galore!, Trimmomatic
- Compartment analysis tool
- CALDER2
- Status
- Under active development (unreleased)
What you can use it for
- Chromatin fraction profiling
- Generate single-track bigWig coverage profiles from sequential solubility fractions to examine chromatin organisation across the genome.
- A/B compartment identification
- Identify higher-order chromosomal A/B compartments from SAMMY-seq data using CALDER2.
- Pairwise fraction comparisons
- Compare signal between different fractions or experimental conditions using SPP or deepTools bigwigCompare.
- Differential solubility analysis
- Detect regions showing altered chromatin solubility across biological groups.
Run it here
The research agent runs nf-core/sammyseq 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.
Strengths and limits
Good at
- Standardises data handling from raw sequence reads to chromatin compartment identification and solubility profiling.
- Provides user choice between BWA and Bowtie 2 for alignment, and between Trim Galore! and Trimmomatic for read trimming.
- Supports both single-end and paired-end sequencing datasets via a structured samplesheet.
- Collects tool statistics and quality metrics across all steps into a unified MultiQC report.
Watch out for
- The pipeline is under active development and has not yet reached a formal release.
- Requires a matching reference genome in FASTA format for read mapping and downstream track production.
Questions
Can I run nf-core/sammyseq without my own cluster?
The research agent runs nf-core/sammyseq 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/sammyseq under?
MIT, like every nf-core pipeline.
What sequencing assay does this pipeline support?
It is designed specifically for Sequential Analysis of MacroMolecules accessibilitY sequencing (SAMMY-seq) data.
Can the pipeline process paired-end reads?
Yes. It accepts both single-end and paired-end FASTQ files defined in the input samplesheet.
Which aligners can be used?
Alignments can be carried out using either BWA or Bowtie 2.
How does the pipeline analyse chromatin compartmentalisation?
It includes an optional step using CALDER2 to identify A/B chromatin compartments across chromosomes.
How to cite it
Lucini, F., Petrini, C., Salviato, E., Pal, K., Rosti, V., Gorini, F., Santarelli, P., Quadri, R., Lembo, G., Graziano, G., Di Patrizio Soldateschi, E., Tagliaferri, I., Pinatel, E., Sebestyén, E., Rotta, L., Gentile, F., Vaira, V., Lanzuolo, C., Ferrari, F., 2024. Biochemical properties of chromatin domains define genome compartmentalization. Nucleic Acids Research 52, e54–e54. https://doi.org/10.1093/nar/gkae454
Written from nf-core/sammyseq's own README. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.