Fastq Python Packages

pyfastx

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

fuc

Frequently used commands in bioinformatics

sequali

Fast sequencing data quality metrics

filterx

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

demultiplex

Versatile FASTA/FASTQ demultiplexer.

dotmatch

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

mercat2

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

fastq-and-furious

Efficient handling of FASTQ files from Python

biobase

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

bioartifact

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

biolic

Placeholder for biolic, a fast streaming bioinformatics toolkit. Python bindings are planned; the tool currently ships as a Rust CLI.

seqseeker

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

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/...)

dnadesign

Python bindings for dnadesign

fastx-barber

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

lrplots

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

fastqwiper

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

readstore-cli

ReadStore Command Line Interface (CLI) Is A Python Package For Accessing Data from the ReadStore API

bio-wrangler

A bioinformatics data wrangling package for FASTA, FASTQ, VCF, and GFF files.

pydemult

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

fast5seek

Get paths for fast5 files contained in BAM, SAM, or fastq.

strandex

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

bio-juno

Juno: read data generator

demort

DEmultiplexing MOnitoring Report Tool