Fastq Python Packages

pyfastx

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

sequali

Fast sequencing data quality metrics

fuc

Frequently used commands in bioinformatics

filterx

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

filemgr

Web file manager for Linux with PAM auth, per-user privilege isolation via setuid, and bioinformatics-friendly previews

biobase

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

fastq-and-furious

Efficient handling of FASTQ files from Python

dnadesign

A lua package for designing DNA.

mercat2

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

fastx-barber

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

readstore-cli

ReadStore Command Line Interface (CLI)

lrplots

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

demultiplex

Versatile FASTA/FASTQ demultiplexer.

pydemult

Streamed and parallel demultiplexing of fastq files in python

strandex

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

fastqwiper

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

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.

demort

DEmultiplexing MOnitoring Report Tool. DEMORT evaluates demultiplexed fastq files by computing various metrics.

fast5seek

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

bio-juno

read data generator

convertfq

Converting DNA to RNA or RNA to DNA in a fastq file

zfq

FastQ file compressor.