SYNOPSIS

fu-rename [options] InputFile.fa [InputFile2.fa ...]

# Rename sequences in a single file
fu-rename input.fa > renamed.fa

# Process multiple files with custom prefix
fu-rename -p 'sample' file1.fa file2.fa > renamed.fa

# Reset counter for each file
fu-rename -r file1.fa file2.fa > renamed.fa

DESCRIPTION

A tool for systematic renaming of sequences in FASTA/FASTQ files. It provides flexible options for naming patterns and maintains sequence quality when processing FASTQ files. The program can handle multiple input files and supports reading from standard input.

PARAMETERS

• -p, --prefix STRING

  New sequence name (accepts placeholders). Default value is "{b}". Available placeholders: {b} = File basename without extensions {B} = File basename with extension

• -s, --separator STRING

  Separator between prefix and sequence number. Default is "."

• -r, --reset

  Reset counter at each file. By default, the counter continues across all files.

• -f, --fasta

  Force FASTA output even for FASTQ input files.

• -n, --nocomments

  Suppress comments in sequence headers.

• -v, --verbose

  Enable verbose output for debugging.

• --version

  Display version information.

FEATURES

• Preserves quality scores when processing FASTQ files
• Supports multiple input files
• Flexible naming patterns with placeholders
• Optional counter reset for each input file
• Maintains compatibility with both FASTA and FASTQ formats

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This suite of tools has been superseded by SeqFu, a compiled program providing faster and safer tools for sequence analysis.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