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FASTQ helpers

FASTQ helpers provide utilities for format conversion, read-length filtering and summarization, quality-score checking, trimming, splitting, and simulation.

Command summary

Command Function Main output
fq2fa Convert FASTQ to FASTA. FASTA file.
fq2txt Extract read sequences from FASTQ. Plain-text sequence file.
fq_len_flt Filter FASTQ reads by length. Kept FASTQ and dropped FASTQ.
fq_len_sum Summarize read-length distribution for one FASTQ file. Length-count table.
fq_length Summarize read lengths for one or more FASTQ/FASTQ.GZ files. Multi-sample length-count table.
fq_split Split an interleaved FASTQ file into paired FASTQ files. R1/R2 FASTQ files.
fq_trim Trim FASTQ reads to a fixed length. Trimmed FASTQ file.
phred_quality Infer quality-score encoding from FASTQ quality characters. Quality format report printed to stdout.
simulate_fastq Generate simulated FASTQ reads. Simulated FASTQ file.

fq2fa

Function

Convert FASTQ records to FASTA format. By default, the original FASTQ read names are preserved. With -n, records are renamed sequentially as t1, t2, and so on.

Parameters

Parameter Meaning
-i Input FASTQ file.
-o Output FASTA file.
-n Assign new sequential read IDs.
-v, --version Print script version.

Examples

fq2fa \
  -i sample.fq \
  -o sample.fa

fq2fa \
  -i sample.fq \
  -n \
  -o sample.renamed.fa

fq2txt

Function

Extract only the sequence line from each FASTQ record and write one sequence per line.

Parameters

Parameter Meaning
-i Input FASTQ file.
-o Output TXT file.
-v, --version Print script version.

Example

fq2txt \
  -i sample.fq \
  -o sample.seq.txt

fq_len_flt

Function

Filter FASTQ reads by sequence length. Reads within the specified length range are written to the output FASTQ file; reads outside the range are written to an additional dropped-read file named <output>.drop.

Parameters

Parameter Meaning
-i Input FASTQ file.
-o Output FASTQ file for retained reads.
-m Minimum read length.
-M Maximum read length.
-v, --version Print script version.

Example

fq_len_flt \
  -i sample.fq \
  -m 25 \
  -M 35 \
  -o sample_25_35.fq

Output files:

sample_25_35.fq
sample_25_35.fq.drop

fq_len_sum

Function

Summarize read-length distribution for a single FASTQ file.

Parameters

Parameter Meaning
-i Input FASTQ file.
-o Output TXT/TSV file.
-v, --version Print script version.

Example

fq_len_sum \
  -i sample.fq \
  -o sample_length_distribution.txt

Output format:

length    reads_number
25        1200
26        1530
...
Total reads number    2730

fq_length

Function

Count read lengths for one or more FASTQ or FASTQ.GZ files and merge the results into one table.

Parameters

Parameter Meaning
-i, --input One or more FASTQ/FASTQ.GZ files.
-o, --output Output file name. Default: fq_length_distr.txt.

Example

fq_length \
  -i sample1.fq.gz sample2.fq.gz sample3.fq.gz \
  -o all_samples_length_distribution.txt

Output columns:

Sample    Length    Read_Count

fq_split

Function

Intended to split an interleaved FASTQ file into paired FASTQ files.

Parameters

Parameter Meaning
-i Input FASTQ or FASTQ.GZ file.
-a Adapter table file. The current implementation accepts this parameter but does not use it internally.
-o Output prefix.
-v, --version Print script version.

Example

fq_split \
  -i interleaved.fq.gz \
  -a adapter.txt \
  -o sample

Expected output naming:

sample.R1.fq
sample.R2.fq

fq_trim

Function

Trim each FASTQ read to a fixed nucleotide length. Reads shorter than the target length are skipped.

Parameters

Parameter Meaning
-i Input FASTQ file.
-o Output trimmed FASTQ file.
-l Target trim length. Default: 30.
-d Declared as “discard reads shorter than minimum length”; in the current implementation, short reads are skipped regardless of this flag.

Example

fq_trim \
  -i sample.fq \
  -l 30 \
  -o sample.trim30.fq

phred_quality

Function

Infer the likely FASTQ quality-score encoding by inspecting quality-score characters from the first N reads.

Parameters

Parameter Meaning
-i, --input Input FASTQ or FASTQ.GZ file.
-n, --number Number of sequences to inspect. Default: 40000.

Example

phred_quality \
  -i sample.fq.gz \
  -n 40000

Example output categories include:

Sanger | Phred+33
Solexa | Solexa+64
Illumina1.3 | Phred+64
Illumina1.5 | Phred+64
Illumina1.8 | Phred+33

simulate_fastq

Function

Generate a simulated FASTQ file with random DNA sequences and random Phred+33 quality strings.

Parameters

Parameter Meaning
-q, --qmin Minimum quality score.
-Q, --qmax Maximum quality score.
-m, --minlen Minimum read length.
-M, --maxlen Maximum read length.
-n, --number Number of reads to generate.
-o, --output Output FASTQ file. Default: simulated.fq.

Example

simulate_fastq \
  -q 30 \
  -Q 40 \
  -m 25 \
  -M 35 \
  -n 100000 \
  -o simulated_25_35.fq

Notes

  • fq_length supports multiple input files and .gz input; fq_len_sum is designed for a single plain FASTQ file.
  • fq_len_flt writes both retained and dropped reads, which is useful for checking whether read-length filtering is too strict.
  • For production pipelines, prefer testing each helper with a small FASTQ subset before running on full sequencing files.