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The Top 23 Python Fastq Open Source Projects

Open source projects categorized as Python Fastq
Basecalling Comparison ⭐ 273
A comparison of different Oxford Nanopore basecallers
most recent commit 5 years ago
Krakentools ⭐ 242
KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
most recent commit 5 months ago
Parallel Fastq Dump ⭐ 224
parallel fastq-dump wrapper
dependent packages 1total releases 9most recent commit a year agopypi parallel-fastq-dump} Downloads
Pyfastx ⭐ 211
a python package for fast random access to sequences from plain and gzipped FASTA/Q files
dependent packages 20total releases 68most recent commit 5 months agopypi pyfastx} Downloads
Fastq Dl ⭐ 174
Download FASTQ files from SRA or ENA repositories.
total releases 5most recent commit 8 months ago
Afterqc ⭐ 157
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
most recent commit 6 years ago
Fastqe ⭐ 152
FASTQ sequence quality visualisation with Emoji
dependent packages 1total releases 6most recent commit 9 months agopypi fastqe} Downloads
Nanopack ⭐ 143
Easily install all nanopack scripts together
total releases 9most recent commit a year ago
Seq2science ⭐ 132
Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.
most recent commit 5 months ago
Viral Ngs ⭐ 129
Viral genomics analysis pipelines
most recent commit 4 years ago
Qiita ⭐ 118
Qiita - A multi-omics databasing effort
total releases 3most recent commit 3 months ago
Ngscheckmate ⭐ 106
Software program for checking sample matching for NGS data
most recent commit 8 months ago
Isoquant ⭐ 98
Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
most recent commit 3 months ago
Fastqp ⭐ 94
Simple FASTQ quality assessment using Python
most recent commit 3 years ago
Pipeline Structural Variation ⭐ 87
Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
most recent commit 2 years ago
Mcclintock ⭐ 83
Meta-pipeline to identify transposable element insertions using next generation sequencing data
most recent commit 3 months ago
Illumina Utils ⭐ 82
A library and collection of scripts to work with Illumina paired-end data (for CASAVA 1.7+ pipeline).
total releases 29most recent commit 4 months ago
Ngsutils ⭐ 80
Tools for next-generation sequencing analysis
most recent commit 5 years ago
Celescope ⭐ 73
Single Cell Analysis Pipelines
total releases 59most recent commit 3 months ago
Neat Genreads ⭐ 72
NEAT read simulation tools
most recent commit 3 years ago
Qcat ⭐ 64
qcat is a Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files.
total releases 3most recent commit 3 years ago
Nanostat ⭐ 63
Create statistic summary of an Oxford Nanopore read dataset
total releases 28most recent commit a year ago
Pyflow Chipseq ⭐ 55
a snakemake pipeline to process ChIP-seq files from GEO or in-house
most recent commit 4 years ago
The 10 Most Depended On Python Fastq Open Source Projects
Pyfastx ⭐ 211
a python package for fast random access to sequences from plain and gzipped FASTA/Q files
dependent packages 20total releases 68latest release November 25, 2023most recent commit 5 months agopypi pyfastx} Downloads
Dnaio ⭐ 52
Efficiently read and write sequencing data from Python
dependent packages 15total releases 23latest release November 20, 2023most recent commit 3 months agopypi dnaio} Downloads
Fastaq ⭐ 45
Python3 scripts to manipulate FASTA and FASTQ files
dependent packages 7total releases 21latest release February 19, 2018most recent commit 2 years agopypi pyfastaq} Downloads
Abstar ⭐ 35
VDJ assignment and antibody sequence annotation. Scalable from a single sequence to billions of sequences.
dependent packages 2total releases 49latest release November 07, 2023most recent commit 5 months agopypi abstar} Downloads
Nanoget ⭐ 10
Functions to extract information from Oxford Nanopore sequencing data and alignments
dependent packages 2total releases 70latest release September 19, 2023most recent commit 7 months agopypi nanoget} Downloads
Fuc ⭐ 38
Frequently used commands in bioinformatics
dependent packages 2total releases 44latest release September 09, 2023most recent commit 7 months agopypi fuc} Downloads
Itsxpress ⭐ 6
Software to trim the ITS region of FASTQ sequences for amplicon sequencing analysis
dependent packages 1total releases 18latest release May 25, 2023most recent commit 4 months agopypi itsxpress} Downloads
Fasta ⭐ 5
This package enables you to deal with biological sequence files easily.
dependent packages 1total releases 20latest release January 18, 2023most recent commit 7 months agopypi fasta} Downloads
Fastqe ⭐ 152
FASTQ sequence quality visualisation with Emoji
dependent packages 1total releases 6latest release April 05, 2021most recent commit 9 months agopypi fastqe} Downloads
Parallel Fastq Dump ⭐ 224
parallel fastq-dump wrapper
dependent packages 1total releases 9latest release April 23, 2019most recent commit a year agopypi parallel-fastq-dump} Downloads
The 10 Latest Releases In Python Fastq Open Source Projects
Pyfastx ⭐ 211
a python package for fast random access to sequences from plain and gzipped FASTA/Q files
dependent packages 20total releases 68latest release November 25, 2023most recent commit 5 months agopypi pyfastx} Downloads
Dnaio ⭐ 52
Efficiently read and write sequencing data from Python
dependent packages 15total releases 23latest release November 20, 2023most recent commit 3 months agopypi dnaio} Downloads
Celescope ⭐ 73
Single Cell Analysis Pipelines
total releases 59latest release November 16, 2023most recent commit 3 months ago
Abstar ⭐ 35
VDJ assignment and antibody sequence annotation. Scalable from a single sequence to billions of sequences.
dependent packages 2total releases 49latest release November 07, 2023most recent commit 5 months agopypi abstar} Downloads
Nanoget ⭐ 10
Functions to extract information from Oxford Nanopore sequencing data and alignments
dependent packages 2total releases 70latest release September 19, 2023most recent commit 7 months agopypi nanoget} Downloads
Fuc ⭐ 38
Frequently used commands in bioinformatics
dependent packages 2total releases 44latest release September 09, 2023most recent commit 7 months agopypi fuc} Downloads
Fastq Dl ⭐ 174
Download FASTQ files from SRA or ENA repositories.
total releases 5latest release August 11, 2023most recent commit 8 months ago
Itsxpress ⭐ 6
Software to trim the ITS region of FASTQ sequences for amplicon sequencing analysis
dependent packages 1total releases 18latest release May 25, 2023most recent commit 4 months agopypi itsxpress} Downloads
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