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

Sequali is a QC tool that generates useful graphs for both short and long-read data.

filterx

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

biobase

A comprehensive package of biological constants, serving as a foundational resource for biology and bioinformatics, complemented by functions to streamline related tasks.

fastq-and-furious

Efficient handling of FASTQ files from Python

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

seqseeker

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

fastx-barber

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

mercat2

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

readstore-cli

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

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.

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.

fastqwiper

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

fast5seek

Subset of fast5 files contained in a fastq, BAM, or SAM file.

pydemult

:fast_forward: 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

demort

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

bio-juno

read data generator

convertfq

convertFQ is used to convert either DNA2RNA or RNA2DNA in a fastq file

zfq

FastQ file compressor