NAME

fu-uniq - Dereplicate sequences and generate abundance information

SYNOPSIS

fu-uniq [options] input.fa > uniq.fa

DESCRIPTION

fu-uniq is a tool for dereplicating DNA sequences and generating abundance information. It identifies unique sequences and can track their abundance using USEARCH-style labels. The tool supports both exact sequence matching and customizable output formats.

Key features: - Dereplicates sequences while maintaining abundance information - Supports USEARCH-style size annotations - Flexible sequence naming options - Handles both FASTA and FASTQ inputs - Processes gzipped files automatically

OPTIONS

Sequence Processing

• -k, --keepname

  Use the name of the first occurrence of each unique sequence as the cluster name. This is useful for maintaining meaningful identifiers. Default: ON

• -m, --min-size N

  Only output sequences that appear at least N times. This helps filter out rare sequences or potential sequencing errors. Default: 0 (no filtering)

• --size-as-comment

  Add size information as a comment rather than part of the sequence name. This affects the format of the output headers. Default: OFF

  Example with option OFF: >seq1;size=10; Example with option ON: >seq1 size=10;

Output Formatting

• -p, --prefix STR

  Prefix for sequence names when not using --keepname. Default: 'seq'

• -s, --separator STR

  Character(s) to separate prefix from sequence number. Default: '.'

• -w, --line-width N

  Width for wrapping FASTA sequence lines. Use 0 for single-line sequences. Default: 80

EXAMPLES

Basic deduplication:

# Find unique sequences and add abundance information
fu-uniq input.fa > uniq.fa

Keep only abundant sequences:

# Keep sequences that appear at least 10 times
fu-uniq -m 10 input.fa > abundant.fa

Custom sequence naming:

# Use custom prefix and separator
fu-uniq -p 'cluster' -s '_' input.fa > clusters.fa

Process multiple files:

# Combine and deduplicate multiple files
fu-uniq file1.fa file2.fa > combined_uniq.fa

Add size as comment:

# Place size information in sequence comment
fu-uniq --size-as-comment input.fa > commented.fa

NOTES

• Memory usage scales with the number of unique sequences
• Sequence comparison is case-insensitive
• Size annotations in input files (;size=N;) are respected and combined

MODERN ALTERNATIVE

This suite of tools has been superseded by SeqFu, a compiled program providing faster and safer tools for sequence analysis. This suite is maintained for the higher portability of Perl scripts under certain circumstances.

SeqFu is available at https://github.com/telatin/seqfu2, and can be installed with BioConda conda install -c bioconda seqfu

CITING

Telatin A, Fariselli P, Birolo G. SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files. Bioengineering 2021, 8, 59. https://doi.org/10.3390/bioengineering8050059