seqfu homocomp

seqfu homocomp collapses each homopolymer run in FASTA or FASTQ sequences to one base. Record names, comments, format, and input order are preserved. For FASTQ records, the first quality score in each collapsed run is retained.

Usage:
  homocomp [options] [<FASTX>...]

Options:
  -t, --threads INT       Number of worker threads [default: 1]
  --batch-size INT        Records processed per worker job [default: 1000]
  -v, --verbose           Print processing information
  -h, --help              Show this help

With no input files, the command reads from standard input. Plain and gzip-compressed FASTA and FASTQ files are supported. Multiple files are emitted in the order given on the command line.

Examples

Compress one FASTQ file:

seqfu homocomp reads.fastq.gz > reads.homocomp.fastq

Process several files with four workers and batches of 5,000 records:

seqfu homocomp reads/*.fastq.gz --threads 4 --batch-size 5000 > combined.fastq

Use a pipe:

seqfu cat reads.fastq.gz | seqfu homocomp > reads.homocomp.fastq

Quality Scores

Input:

@read comment
AAACCCGTTTTA
+
123456789ABC

Output:

@read comment
ACGTA
+
1478C

The old standalone fu-homocomp executable has been removed; use seqfu homocomp instead.