readfx
ReadFX
ReadFX is a Nim library for parsing FASTQ/FASTA files with high performance.
ReadFX is a Nim library for parsing FASTA and FASTQ files (collectively known as FASTX). It combines two approaches to sequence file parsing:
- A Nim wrapper around Heng Li’s kseq.h C library (klib)
- A native Nim implementation (nimklib)
Both implementations provide efficient parsing with different tradeoffs in terms of performance and memory usage.
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.sequence.len
# 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
Key Features
- Support for both FASTA and FASTQ formats
- Automatic handling of gzipped files
- Memory-efficient parsing options
- Support for reading from stdin using “-“ as filename
Documentation
Notes
- Methods - Detailed documentation of all available methods
- Utils methods - Utility methods for manipulating sequence records
- Data Structure - Overview of internal data structures
-
Parsing algorithms - Details about the parsing implementation
- Repository Structure - Overview of the project organization
- API Reference - Detailed API documentation