genbank

There are 87 repositories under genbank topic.

  • kblin/ncbi-genome-download

    Scripts to download genomes from the NCBI FTP servers

    Language:Python95635145175
  • poly

    bebop/poly

    A Go package for engineering organisms.

    Language:Go6771316573

  • Edinburgh-Genome-Foundry/DnaFeaturesViewer

    :eye: Python library to plot DNA sequence features (e.g. from Genbank files)

    Language:Python601197492
  • pyGenomeViz

    moshi4/pyGenomeViz

    A genome visualization python package for comparative genomics

    Language:Python28534523
  • pydna

    BjornFJohansson/pydna

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

    Language:Jupyter Notebook1661315245

  • 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:Shell14614315

  • eead-csic-compbio/get_homologues

    GET_HOMOLOGUES: a versatile software package for pan-genome analysis

    Language:Perl1101711726

  • pirovc/ganon

    ganon2 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:Python8746713

  • mtisza1/Cenote-Taker2

    Cenote-Taker2: Discover and Annotate Divergent Viral Contigs (Please use Cenote-Taker 3 instead)

    Language:Shell542497

  • rcs333/VAPiD

    VAPiD: Viral Annotation and Identification Pipeline

    Language:Shell5141415

  • nextstrain/mpox

    Nextstrain build for mpox virus

    Language:Python45185619

  • nextstrain/ncov-ingest

    A 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:Python36189620

  • maximilianh/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:Python35432

  • jperkel/gb_read

    An example GenBank file reader in Rust

    Language:Rust34327

  • CDCgov/seqsender

    Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories

    Language:HTML3252711

  • CDCgov/tostadas

    🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission

    Language:Python2751177

  • Koeng101/dnadesign

    A Go package for designing DNA.

    Language:Go264460

  • ropensci/restez

    :sleeping: :open_file_folder: Create and Query a Local Copy of GenBank in R

    Language:R258435

  • bebop/ark

    Go REST API to replace Genbank, Uniprot, Rhea, and CHEMBL

    Language:Go235556

  • fsprojects/BioProviders

    F# library for accessing and manipulating bioinformatic datasets.

    Language:F#233100
  • GBKviz

    moshi4/GBKviz

    Easy-to-use web application for visualization and comparison of genomes in Genbank file

    Language:Python23204

  • ropensci/phylotaR

    An automated pipeline for retrieving orthologous DNA sequences from GenBank in R

    Language:R236709

  • wpwupingwp/OGU

    a toolbox for utilize organelle genomic data

    Language:Python23151

  • Edinburgh-Genome-Foundry/SnapGeneReader

    👓 Python library to parse Snapgene *.dna files to dict or biopython seqrecord.

    Language:Python18606

  • BioJulia/GenomicAnnotations.jl

    Language:Julia167144

  • biosustain/goodbye-genbank

    A Python package for Biopython that gives feature annotations from GenBank records a new and better life

    Language:Python14503

  • dlesl/gb-io

    A Rust library for parsing, writing and manipulating Genbank sequence files

    Language:Rust14255

  • mtisza1/Cenote-Taker

    DEPRECATED: Use Cenote-Taker 3 instead

    Language:Shell14102

  • HobnobMancer/cazy_webscraper

    Web scraper to retrieve protein data catalogued by the CAZy, UniProt, NCBI, GTDB and PDB websites/databases.

    Language:Python123592

  • Lattice-Automation/seqparse

    Parse sequence files (GenBank, FASTA, SnapGene, SBOL) and accession IDs (NCBI, iGEM) to a common format

    Language:TypeScript11353
  • worst-genbank-ever

    TimothyStiles/worst-genbank-ever

    The most awful genbank file you'll ever need to parse.

    9300

  • 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:Python81105

  • michellejlin/lava

    LAVA: Longitudinal Analysis of Viral Alleles

    Language:Python8207

  • Changwanseo/GenMine

    GenBank Record downloader for taxonomists

    Language:Python7100

  • j-i-l/GenBankParser

    Parser (unofficial) for ncbi GenBank data

    Language:Python7513

  • 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:Perl6117