genbank
There are 2 repositories under genbank topic.
kblin / ncbi-genome-download
Scripts to download genomes from the NCBI FTP servers
Language:Python 914- polyLanguage:Go 661
Edinburgh-Genome-Foundry / DnaFeaturesViewer
:eye: Python library to plot DNA sequence features (e.g. from Genbank files)
Language:Python 576- pyGenomeViz
moshi4 / pyGenomeViz
A genome visualization python package for comparative genomics
Language:Python 254 - pydna
BjornFJohansson / pydna
Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.
Language:Jupyter Notebook 160 pirovc / genome_updater
Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy
Language:Shell 136eead-csic-compbio / get_homologues
GET_HOMOLOGUES: a versatile software package for pan-genome analysis
Language:Perl 104ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more
Language:Python 84mtisza1 / Cenote-Taker2
Cenote-Taker2: Discover and Annotate Divergent Viral Contigs (Please use Cenote-Taker 3 instead)
Language:Shell 57- Language:Shell 50
nextstrain / mpox
Nextstrain build for mpox virus
Language:Python 39maximilianh / multiSub
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.
Language:Python 35A pipeline that ingests SARS-CoV-2 (i.e. nCoV) data from GISAID and Genbank, transforms it, stores it on S3, and triggers Nextstrain nCoV rebuilds.
Language:Python 35- Language:Rust 34
CDCgov / seqsender
Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories
Language:Python 32- Language:R 25
🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission
Language:Python 23- Language:R 23
- Language:Go 22
fsprojects / BioProviders
F# library for accessing and manipulating bioinformatic datasets.
Language:F# 22- Language:Go 21
- Language:Python 21
- GBKviz
Easy-to-use web application for visualization and comparison of genomes in Genbank file
Language:Python 20 đź‘“ Python library to parse Snapgene *.dna files to dict or biopython seqrecord.
Language:Python 18- Language:Julia 14
biosustain / goodbye-genbank
A Python package for Biopython that gives feature annotations from GenBank records a new and better life
Language:Python 14DEPRECATED: Use Cenote-Taker 3 instead
Language:Shell 14- Language:Rust 13
HobnobMancer / cazy_webscraper
Web scraper to retrieve protein data catalogued by the CAZy, UniProt, NCBI, GTDB and PDB websites/databases.
Language:Python 13Lattice-Automation / seqparse
Parse sequence files (GenBank, FASTA, SnapGene, SBOL) and accession IDs (NCBI, iGEM) to a common format
Language:TypeScript 9- worst-genbank-ever
TimothyStiles / worst-genbank-ever
The most awful genbank file you'll ever need to parse.
bfosso / MetaShot
MetaShot (Metagenomics Shotgun) is a complete pipeline designed for the taxonomic classification of the human microbiota members. In MetaShot, third party tools and new developed Python and Bash scripts are integrated to analyze paired-end (PE) Illumina sequences, offering an automated procedure covering all the analysis steps from raw data management to taxonomic profiling. It is designed to analyze both DNA-Seq and RNA-Seq data.
Language:Python 8michellejlin / lava
LAVA: Longitudinal Analysis of Viral Alleles
Language:Python 8- Language:Python 7
- Language:Python 7
terrimporter / COI_NCBI_2018
This repository contains the scripts used to retrieve and analyze the data reported in Porter & Hajibabaei 2018 bioRxiv doi: https://doi.org/10.1101/353904
Language:Perl 6
