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The Top 23 Python Fasta Open Source Projects

Open source projects categorized as Python Fasta
Esm ⭐ 2,577
Evolutionary Scale Modeling (esm): Pretrained language models for proteins
dependent packages 14total releases 12most recent commit 3 months agopypi fair-esm} Downloads
Biotite ⭐ 515
A comprehensive library for computational molecular biology
dependent packages 21total releases 52most recent commit 3 months agopypi biotite} Downloads
Pyfaidx ⭐ 427
Efficient pythonic random access to fasta subsequences
dependent packages 119total releases 86most recent commit 3 months agopypi pyfaidx} Downloads
Krakentools ⭐ 242
KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
most recent commit 5 months ago
Cdna_cupcake ⭐ 224
Miscellaneous collection of Python and R scripts for processing Iso-Seq data
most recent commit 9 months ago
Vcf2phylip ⭐ 216
Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
most recent commit 10 months ago
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
Vamb ⭐ 205
Variational autoencoder for metagenomic binning
total releases 13most recent commit 4 months ago
Pydna ⭐ 140
Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.
dependent packages 7total releases 110most recent commit 4 months agopypi pydna} Downloads
Badread ⭐ 124
a long read simulator that can imitate many types of read problems
most recent commit 4 months ago
Redundans ⭐ 121
Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.
most recent commit 4 months ago
Chiron ⭐ 114
A basecaller for Oxford Nanopore Technologies' sequencers
total releases 24most recent commit a year ago
Dna2vec ⭐ 103
dna2vec: Consistent vector representations of variable-length k-mers
most recent commit 4 years ago
Isoquant ⭐ 98
Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
most recent commit 4 months ago
Bcalm ⭐ 90
compacted de Bruijn graph construction in low memory
most recent commit a year ago
Mcclintock ⭐ 83
Meta-pipeline to identify transposable element insertions using next generation sequencing data
most recent commit 3 months ago
Deblur ⭐ 83
Deblur is a greedy deconvolution algorithm based on known read error profiles.
total releases 15most recent commit 9 months ago
Mummer2circos ⭐ 79
Circular bacterial genome plots based on BLAST or NUCMER/PROMER alignments
most recent commit 4 months ago
Pyfasta ⭐ 77
fast, memory-efficient, pythonic (and command-line) access to fasta sequence files
dependent packages 9total releases 25most recent commit 6 years agopypi pyfasta} Downloads
Wgd ⭐ 74
Python package and CLI for whole-genome duplication related analyses
most recent commit 7 months ago
Pav ⭐ 68
Phased assembly variant caller
most recent commit 6 months ago
Aviary ⭐ 62
A hybrid assembly and MAG recovery pipeline (and more!)
total releases 19most recent commit 3 months ago
Plasflow ⭐ 61
Software for prediction of plasmid sequences in metagenomic assemblies
total releases 5most recent commit 3 years ago
The 10 Most Depended On Python Fasta Open Source Projects
Pyfaidx ⭐ 427
Efficient pythonic random access to fasta subsequences
dependent packages 119total releases 86latest release September 22, 2023most recent commit 3 months agopypi pyfaidx} Downloads
Biotite ⭐ 515
A comprehensive library for computational molecular biology
dependent packages 21total releases 52latest release September 09, 2023most recent commit 3 months agopypi biotite} Downloads
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
Esm ⭐ 2,577
Evolutionary Scale Modeling (esm): Pretrained language models for proteins
dependent packages 14total releases 12latest release October 18, 2022most recent commit 3 months agopypi fair-esm} Downloads
Pyfasta ⭐ 77
fast, memory-efficient, pythonic (and command-line) access to fasta sequence files
dependent packages 9total releases 25latest release April 03, 2014most recent commit 6 years agopypi pyfasta} 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
Smof ⭐ 12
Explore and analyze biological sequence data
dependent packages 2total releases 12latest release July 18, 2022most recent commit a year agopypi smof} Downloads
Fuc ⭐ 38
Frequently used commands in bioinformatics
dependent packages 2total releases 44latest release September 09, 2023most recent commit 8 months agopypi fuc} Downloads
The 10 Latest Releases In Python Fasta 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
Aviary ⭐ 62
A hybrid assembly and MAG recovery pipeline (and more!)
total releases 19latest release November 20, 2023most recent commit 3 months ago
Pyfaidx ⭐ 427
Efficient pythonic random access to fasta subsequences
dependent packages 119total releases 86latest release September 22, 2023most recent commit 3 months agopypi pyfaidx} Downloads
Fdog ⭐ 8
Feature-aware Directed OrtholoG search
dependent packages 1total releases 68latest release September 19, 2023most recent commit 4 months agopypi fdog} Downloads
Biotite ⭐ 515
A comprehensive library for computational molecular biology
dependent packages 21total releases 52latest release September 09, 2023most recent commit 3 months agopypi biotite} Downloads
Fuc ⭐ 38
Frequently used commands in bioinformatics
dependent packages 2total releases 44latest release September 09, 2023most recent commit 8 months agopypi fuc} Downloads
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