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Search results for python fasta

249 search results found

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

Biotite ⭐ 515

A comprehensive library for computational molecular biology

Pyfaidx ⭐ 427

Efficient pythonic random access to fasta subsequences

Krakentools ⭐ 242

KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files

Cdna_cupcake ⭐ 224

Miscellaneous collection of Python and R scripts for processing Iso-Seq data

Vcf2phylip ⭐ 216

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

Pyfastx ⭐ 211

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

Variational autoencoder for metagenomic binning

Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.

Badread ⭐ 124

a long read simulator that can imitate many types of read problems

Redundans ⭐ 121

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.

A basecaller for Oxford Nanopore Technologies' sequencers

Dna2vec ⭐ 103

dna2vec: Consistent vector representations of variable-length k-mers

Isoquant ⭐ 98

Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)

compacted de Bruijn graph construction in low memory

Mcclintock ⭐ 83

Meta-pipeline to identify transposable element insertions using next generation sequencing data

Deblur is a greedy deconvolution algorithm based on known read error profiles.

Mummer2circos ⭐ 79

Circular bacterial genome plots based on BLAST or NUCMER/PROMER alignments

fast, memory-efficient, pythonic (and command-line) access to fasta sequence files

Python package and CLI for whole-genome duplication related analyses

Phased assembly variant caller

A hybrid assembly and MAG recovery pipeline (and more!)

Plasflow ⭐ 61

Software for prediction of plasmid sequences in metagenomic assemblies

Emblmygff3 ⭐ 57

An efficient way to convert gff3 annotation files into EMBL format ready to submit.

Flexidot ⭐ 56

Highly customizable, ambiguity-aware dotplots for visual sequence analyses

Efficiently read and write sequencing data from Python

Predict AMPs in (meta)genomes and peptides

A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome

Python3 scripts to manipulate FASTA and FASTQ files

Prothint ⭐ 45

Protein hint generation pipeline for gene finding in eukaryotic genomes

Yet Another Motif Discovery Algorithm

tools for error correction and working with long read data

Detection of viruses from RNA-Seq on human samples

Fast and accurate set similarity estimation via containment min hash

Rnasamba ⭐ 41

A tool for computing the coding potential of RNA transcript sequences using deep learning classification model

Frequently used commands in bioinformatics

ProFET: Protein Feature Engineering Toolkit for Machine Learning

SV genotyping with long reads

Deep learning library for biological sequences. Extension of Fastai and Pytorch.

Popgen Stats ⭐ 32

Scripts to calculate population genetics statistics

Chromosomer ⭐ 30

A reference-assisted assembly tool for producing draft chromosome sequences.

Justorthologs ⭐ 30

Factornet ⭐ 30

A deep learning package for predicting TF binding

Tmhmm.py ⭐ 30

A transmembrane helix finder in Python 3.

Concordance and contamination estimator for tumor–normal pairs

HMM-based identification and categorization of iron genes and iron gene operons in genomes and metagenomes

Computational pipeline for calling consensi on R2C2 nanopore data

Multisub ⭐ 28

Prepares a SARS-CoV-2 submission for GISAID, NCBI or ENA. Can read GISAID or NCBI files, or plain fasta+tsv/csv/xls. Finds files in input directory and merges everything into a single output directory. Auto-detects input file formats. Can submit the results to multiple repositories from the command line.

Chromatiblock ⭐ 28

Colinear block visualisation tool

RADIA: RNA and DNA Integrated Analysis for Somatic Mutation Detection

VAPiD: Viral Annotation and Identification Pipeline

Public Health England SNP calling pipeline.

Demultiplex ⭐ 26

Versatile FASTA/FASTQ demultiplexer.

Spraynpray ⭐ 25

Rapid and simple taxonomic profiling of genome and metagenome contigs

Vcf2fasta ⭐ 25

Converts a VCF file to a FASTA alignment provided a reference genome and a GFF file

Fast and flexible ORF finder

Metasanity ⭐ 24

Pipeline for major biological analyses.

Public_scripts ⭐ 24

collection of bioinformatic scripts

Plasclass ⭐ 23

A tool to classify sequences of plasmid or chromosomal origin. A paper describing this tool is available at: https://journals.plos.org/ploscompbiol/article?id=

Autopvs1 ⭐ 23

An automatic classification tool for PVS1 interpretation of null variants

This repository is deprecated, please use the link to the right.

Deeph3 Distances Orientations ⭐ 23

Order and orientation of complete bacterial genomes

UniProt Id Mapping through API

GC Skew Test for Bacterial Genomes

Pseudogenepipeline ⭐ 22

Mic_prediction ⭐ 22

Code for doing MIC predictions on genomes

SMBL - SnakeMake Bioinformatics Library. Automatic installation of bioinformatics software in your SnakeMake pipelines.

Swiftortho ⭐ 21

A high performance tool to identify orthologs and paralogs across genomes.

Biohansel ⭐ 21

Rapidly subtype microbial genomes using single-nucleotide variant (SNV) subtyping schemes

whole genome MLST analysis

AMBER: Assessment of Metagenome BinnERs

Contiguator ⭐ 20

Bacterial genomes finishing tool for structural insights on draft genomes

Deepdist ⭐ 19

Deep learning prediction of protein residue-residue distances

Metagenomic binning using low-density hashing a support vector machine

Shortbred ⭐ 19

ShortBRED is a pipeline to take a set of protein sequences, reduce them to a set of unique identifying strings ("markers"), and then search for these markers in metagenomic data and determine the presence and abundance of the protein families of interest.

For original Nature Biotechnology Publication (Q1 2012)

Crispridentify ⭐ 18

Flu Prediction ⭐ 18

Predicting Future Influenza Virus Sequences with Machine Learning

Bionitio Python ⭐ 18

Demonstrating best practices for bioinformatics command line tools

Reads For Assembly ⭐ 17

Simulate metagenomic short reads from one or more populations.

Read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC)

Report reverse and ambiguous strand SNPs in GWAS data

Binf_toolkit ⭐ 17

Handy scripts for routine bioinformatic analysis

🎯 Generate DNA sequences with specified amino acid, codon, and k-mer frequencies

Local Lineage and Monophyly Assessment

Core Genome Alignment ⭐ 16

Scripts to analyze gene content and make a concatenated alignment of core genes from bacterial genomes.

Junction centric alternative splicing translator

Kmer2snp ⭐ 16

Protein orthologous group assignment with deep learning

Storf Reporter ⭐ 15

Package to extract Unannotated Regions from prokaryotic genomes report coding and pseudogenised genes delimited by stop codons - Named StORFs (Stop - Open Reading Frames)

Ngs Protocols ⭐ 15

Scripts to run several protocols to process and analyze Next-Generation Sequencing data

Reduction of Althaps and Duplicate Contigs for Improved Hi-C Scaffolding

TEspeX - pipeline for Transposable Elements expression quantification

Enasearch ⭐ 15

A Python library for interacting with ENA's API

Dna2proteins ⭐ 15

A Python script to translate DNA sequences to protein sequences

Implementation of a polymorphism aware phylogenetic model using HYPHY

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