readfx

Parse FASTQ and FASTA files, using Heng Li's Klib

Pure Nim score 30/100 · tests present · docs generated

Summary

Latest Version 0.6.0
License MIT
CI Status Failing
Downloads 0
Last Indexed 2026-08-27 06:49

Tags

fasta fastq fastx seqfu bioinformatics parser kseq readfq

Authors

  • Andreas Wilm and SeqFu team

Installation

nimble install readfx
choosenim install readfx
git clone https://github.com/quadram-institute-bioscience/readfx

OS Compatibility

Platform Linux macOS Windows FreeBSD OpenBSD NetBSD Android iOS WASM Embedded
readfx ✓ ✓ ✓ - - - - - - -

Dependencies

Package Version Optional
nim >= 2.2.0", "gzfast >= 0.2.2 No

Source

Repository https://github.com/quadram-institute-bioscience/readfx
Homepage https://github.com/quadram-institute-bioscience/readfx
Documentation View Documentation
Registry Source nimble_official

README

ReadFX - Nim FASTQ/FASTA Parser

Nim Tests

The Nim FASTA/FASTQ parsing library for SeqFu.

Installation

nimble install readfx

Usage

import readfx

# Using the C wrapper (klib)
for record in readFQ("example.fastq"):
  echo record.name, ": ", record.sequence.len

# Using pointer-based version (more efficient, reuses memory)
for record in readFQPtr("example.fastq.gz"):
  echo $record.name, ": ", record.sequenceLen

# Using the native Nim implementation
var r: FQRecord
var f = xopen[GzFile]("example.fastq.gz")
defer: f.close()
while f.readFastx(r):
  echo r.name, ": ", r.sequence.len

# Reading paired-end FASTQ files
for pair in readFQPair("sample_R1.fastq.gz", "sample_R2.fastq.gz"):
  echo "R1: ", pair.read1.name, " (", pair.read1.sequence.len, " bp)"
  echo "R2: ", pair.read2.name, " (", pair.read2.sequence.len, " bp)"

# Pointer-based paired-end iteration (zero-copy, pointers are reused)
for pair in readFQPairPtr("sample_R1.fastq.gz", "sample_R2.fastq.gz"):
  echo "Pair length: ", pair.read1.sequenceLen + pair.read2.sequenceLen

# Pointer-based interleaved paired-end iteration
for pair in readFQInterleavedPairPtr("sample.interleaved.fastq.gz", checkNames = true):
  echo "Pair length: ", pair.read1.sequenceLen + pair.read2.sequenceLen

# String-based interleaved paired-end iteration (safe to store records)
for pair in readFQInterleavedPair("sample.interleaved.fastq.gz", checkNames = true):
  echo "R1: ", pair.read1.name, " / R2: ", pair.read2.name

FQRecordPtr now includes cached nameLen, commentLen, sequenceLen, and qualityLen fields. These lengths exclude the trailing NUL terminator and avoid repeated cstring scans in pointer-heavy code. Because FQRecordPtr layout changed, downstream projects must be recompiled after upgrading to this release.

Authors