bb_fastq_to_fasta - ampinzonv/BB3 GitHub Wiki
Function: bb_fastq_to_fasta
Convert a FASTQ file to FASTA format.
๐ Description
This function extracts the sequence and identifier lines from a FASTQ file and converts them into FASTA format.
๐ฅ Input
- A FASTQ file with sequencing reads.
- STDIN is supported via
--input -.
๐ค Output
- A FASTA-formatted stream or file.
๐งช Examples
bb_fastq_to_fasta --input reads.fastq
cat reads.fastq | bb_fastq_to_fasta --input -
bb_fastq_to_fasta --input reads.fastq --outfile reads.fasta
โ๏ธ Usage
bb_fastq_to_fasta --input FILE [--outfile FILE] [--quiet] [--force]
๐งต Options
| Option | Description |
|---|---|
--input FILE |
Input FASTQ file or - for STDIN (required) |
--outfile FILE |
Output FASTA file (optional, default: STDOUT) |
--quiet |
Suppress informational messages |
--force |
Overwrite output file if it exists |
๐ Notes
- This function ignores the quality lines from the FASTQ file.
- Useful for compatibility with FASTA-only tools or pipelines.