Fastq Python Packages

pyfastx

a python package for fast random access to sequences from plain and gzipped FASTA/Q files

dotmatch

Fast exact short-DNA known-target assignment for CRISPR guides, barcodes, primers, panels, and whitelists.

sequali

Fast sequencing data quality metrics

filterx

process any file in tabular format. Fasta/fastq/GTF/GFF/VCF/SAM/BED

fuc

Frequently used commands in bioinformatics

fastq-and-furious

Efficient handling of FASTQ files from Python

fqxv

Rust-based FASTQ archiving

nanotimesort

Bin Oxford Nanopore reads by cumulative sequencing time intervals. Guppy, MinKNOW and Dorado compatible. Fast, streaming, zero dependencies.

mercat2

MerCat2: python code for versatile k-mer counting and diversity estimation for database independent property analysis for metaome data

biobase

A home for all biological/bioinformatics constants from protein strings to BLOSUM matrices.

kingfisher

Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.

dnadesign

A lua package for designing DNA.

demultiplex

Versatile FASTA/FASTQ demultiplexer.

filemgr

Web file manager for Linux servers with PAM auth, per-user privilege isolation via setuid, fuzzy search, recycle bin, bio-file-aware previews (fastq/bam/vcf/...)

readstore-cli

ReadStore Command Line Interface (CLI)

bioartifact

Lightweight, agent-friendly inspection and contract validation for bioinformatics artifacts.

fastx-barber

Python package to trim and extract flags from FASTA and FASTQ files.

strandex

Sample an approximate number of reads from a fastq file without reading the entire file

lrplots

A collection of plots for long read sequencing FastQ files from devices like Oxford Nanopore's MinION and PromethION.

bio-wrangler

Bio-Wrangler is a Python package for bioinformatics data wrangling. It helps load, filter, merge, and summarize bioinformatics datasets from formats like FASTA, FASTQ, VCF, and GFF.

biolic

A fast, modular, streaming bioinformatics toolkit in Rust for FASTQ/FASTA/BAM — a platform that grows through modules, with strong long-read support.

pydemult

:fast_forward: Streamed and parallel demultiplexing of fastq files in python

fastqwiper

An ensemble method to recover corrupted FASTQ files, drop or fix pesky lines, remove unpaired reads, and settle reads interleaving.

seqseeker

Fast k-mer–based detection of any target sequence in paired single-cell FASTQ files