low-complexity-nextflow

A Nextflow pipeline that masks low-complexity regions in nucleotide or protein sequences.

Overview

This pipeline identifies low-complexity regions in an input FASTA file using NCBI's dustmasker (for nucleotide sequences) or seg (for protein sequences), and produces a sorted, indexed BED file of the masked intervals. It is used within VEuPathDB's genome annotation workflows to flag low-complexity regions of a genome or proteome so they can be excluded from or annotated separately in downstream analyses such as similarity searches. The input FASTA is split into subsets for parallel masking, the raw interval output is converted to BED coordinates, and the combined results are sorted, compressed with bgzip, and indexed with tabix.

Requirements

• Nextflow (DSL2)
• Docker (a docker.config profile is included; singularity and lsf config files are also provided)

The pipeline uses the veupathdb/blastsimilarity:1.0.0 container (built from the included Dockerfile, which extends veupathdb/blastsimilarity with the seg tool) for masking, and bioperl/bioperl:stable and biocontainers/tabix:v1.9-11-deb_cv1 for BED conversion and indexing.

Usage

The pipeline provides two built-in Nextflow profiles that select the input sequence type and masking program: aa (protein sequences, masked with seg) and na (nucleotide sequences, masked with dustmasker).

nextflow run VEuPathDB/low-complexity-nextflow \
  -r main \
  -profile na,docker \
  --inputFilePath /path/to/genome.fa \
  --outputDir /path/to/output \
  --outputFileName lowComplexity-na.bed \
  -resume

The pipeline has a single, unnamed workflow entry point that runs the full process: splitting the input FASTA, masking each subset with the program selected by params.seqType, converting the results to BED, and sorting/compressing/indexing the output.

Key Parameters

Parameter	Description
params.inputFilePath	Path to the input FASTA file (nucleotide or protein) to mask.
params.seqType	Sequence type: aa (protein, masked with seg) or na (nucleotide, masked with dustmasker); set automatically by the aa/na profiles.
params.fastaSubsetSize	Number of sequences per FASTA subset sent to a single masking process; controls the degree of parallelism.
params.outputFileName	File name for the final BED output (e.g. lowComplexity-na.bed or lowComplexity-aa.bed).
params.outputDir	Directory where the final .bed.gz and .tbi index are published.

Output

A bgzip-compressed, tabix-indexed BED file (<outputFileName>.gz and its .tbi index) listing the low-complexity intervals found across the input sequences, sorted by sequence and start coordinate.