genbank | Topic | Ecosyste.ms: Repos

Topic: "genbank"

kblin/ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers

Language: Python - Size: 347 KB - Last synced at: 3 days ago - Pushed at: 12 months ago - Stars: 1,023 - Forks: 177

bebop/poly

A Go package for engineering organisms.

Language: Go - Size: 11 MB - Last synced at: 3 days ago - Pushed at: 9 months ago - Stars: 709 - Forks: 71

Edinburgh-Genome-Foundry/DnaFeaturesViewer

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

Language: Python - Size: 15.6 MB - Last synced at: 21 days ago - Pushed at: 23 days ago - Stars: 640 - Forks: 100

moshi4/pyGenomeViz

A genome visualization python package for comparative genomics

Language: Python - Size: 74.9 MB - Last synced at: 19 days ago - Pushed at: 2 months ago - Stars: 341 - Forks: 21

pydna-group/pydna

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

Language: Python - Size: 57.4 MB - Last synced at: about 24 hours ago - Pushed at: 1 day ago - Stars: 182 - Forks: 47

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 - Size: 1.29 MB - Last synced at: 3 months ago - Pushed at: 7 months ago - Stars: 154 - Forks: 15

eead-csic-compbio/get_homologues

GET_HOMOLOGUES: a versatile software package for pan-genome analysis

Language: Perl - Size: 79.8 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 116 - Forks: 27

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: Python - Size: 24.2 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 96 - Forks: 12

mtisza1/Cenote-Taker2

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

Language: Shell - Size: 62.3 MB - Last synced at: 4 months ago - Pushed at: over 1 year ago - Stars: 55 - Forks: 7

rcs333/VAPiD

VAPiD: Viral Annotation and Identification Pipeline

Language: Shell - Size: 18 MB - Last synced at: 4 months ago - Pushed at: about 1 year ago - Stars: 52 - Forks: 15

nextstrain/mpox

Nextstrain build for mpox virus

Language: Python - Size: 33.3 MB - Last synced at: 2 days ago - Pushed at: 3 days ago - Stars: 49 - Forks: 22

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: Python - Size: 402 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 37 - Forks: 20

CDCgov/seqsender

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

Language: Python - Size: 261 MB - Last synced at: 3 months ago - Pushed at: 4 months ago - Stars: 35 - Forks: 14

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: Python - Size: 1020 KB - Last synced at: 12 months ago - Pushed at: about 3 years ago - Stars: 35 - Forks: 2

jperkel/gb_read

An example GenBank file reader in Rust

Language: Rust - Size: 85 KB - Last synced at: over 2 years ago - Pushed at: about 4 years ago - Stars: 34 - Forks: 7

Koeng101/dnadesign

A Go package for designing DNA.

Language: Go - Size: 37.1 MB - Last synced at: 30 days ago - Pushed at: 30 days ago - Stars: 32 - Forks: 1

CDCgov/tostadas

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

Language: Python - Size: 49.4 MB - Last synced at: 3 days ago - Pushed at: 4 days ago - Stars: 28 - Forks: 14

ropensci/restez

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

Language: R - Size: 10 MB - Last synced at: 2 days ago - Pushed at: 5 months ago - Stars: 27 - Forks: 5

Edinburgh-Genome-Foundry/SnapGeneReader Fork of IsaacLuo/SnapGeneFileReader

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

Language: Python - Size: 644 KB - Last synced at: 12 days ago - Pushed at: 3 months ago - Stars: 25 - Forks: 7

wpwupingwp/OGU

a toolbox for utilize organelle genomic data

Language: Python - Size: 1.78 MB - Last synced at: 20 days ago - Pushed at: 28 days ago - Stars: 24 - Forks: 1

fsprojects/BioProviders

F# library for accessing and manipulating bioinformatic datasets.

Language: F# - Size: 251 MB - Last synced at: 17 days ago - Pushed at: over 1 year ago - Stars: 24 - Forks: 0

bebop/ark

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

Language: Go - Size: 17 MB - Last synced at: 5 days ago - Pushed at: over 1 year ago - Stars: 23 - Forks: 6

ropensci/phylotaR

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

Language: R - Size: 15.3 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 23 - Forks: 8

moshi4/GBKviz 📦

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

Language: Python - Size: 5.25 MB - Last synced at: about 1 month ago - Pushed at: about 3 years ago - Stars: 21 - Forks: 4

dlesl/gb-io

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

Language: Rust - Size: 3.67 MB - Last synced at: 26 days ago - Pushed at: 3 months ago - Stars: 20 - Forks: 5

Lattice-Automation/seqparse

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

Language: TypeScript - Size: 4.89 MB - Last synced at: 29 days ago - Pushed at: about 1 year ago - Stars: 17 - Forks: 4

BioJulia/GenomicAnnotations.jl

Language: Julia - Size: 5.03 MB - Last synced at: 7 days ago - Pushed at: 5 months ago - Stars: 16 - Forks: 4

HobnobMancer/cazy_webscraper

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

Language: Python - Size: 46.7 MB - Last synced at: 18 days ago - Pushed at: 7 months ago - Stars: 14 - Forks: 2

mtisza1/Cenote-Taker

DEPRECATED: Use Cenote-Taker 3 instead

Language: Shell - Size: 147 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 14 - Forks: 2

biosustain/goodbye-genbank

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

Language: Python - Size: 284 KB - Last synced at: 6 days ago - Pushed at: about 9 years ago - Stars: 14 - Forks: 3

karubiotools/getSequenceInfo Fork of dcouvin/getSequenceInfo

Perl and Python scripts allowing to get sequence information from GenBank, RefSeq or ENA sequence repositories

Language: Perl - Size: 14.7 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 12 - Forks: 4

TimothyStiles/worst-genbank-ever

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

Size: 14.6 KB - Last synced at: 4 months ago - Pushed at: over 1 year ago - Stars: 9 - Forks: 0

michellejlin/lava

LAVA: Longitudinal Analysis of Viral Alleles

Language: Python - Size: 53.5 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 8 - Forks: 7

Changwanseo/GenMine

GenBank Record downloader for taxonomists

Language: Python - Size: 446 KB - Last synced at: 1 day ago - Pushed at: about 1 month ago - Stars: 7 - Forks: 0

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 - Size: 1.54 MB - Last synced at: almost 2 years ago - Pushed at: about 5 years ago - Stars: 7 - Forks: 5

j-i-l/GenBankParser

Parser (unofficial) for ncbi GenBank data

Language: Python - Size: 208 KB - Last synced at: 4 months ago - Pushed at: over 5 years ago - Stars: 7 - Forks: 3

Robaina/GenBankpy

Tools to download, parse and filter GenBank files

Language: Python - Size: 25 MB - Last synced at: 6 days ago - Pushed at: over 2 years ago - Stars: 5 - Forks: 1

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 - Size: 46.9 KB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 5 - Forks: 7

moltinginstar/addgene-api

An unofficial API for Addgene, the open-source plasmid repository.

Language: Python - Size: 26.4 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 4 - Forks: 1

santiagosnchez/gb2fasta

Perl script to convert GenBank records to FASTA format

Language: Perl - Size: 17.6 KB - Last synced at: almost 2 years ago - Pushed at: about 4 years ago - Stars: 4 - Forks: 0

SMRUCC/GCModeller.Core

GCModeller Individual Components: GCModeller base core assembly library on common biological database read and write I/O

Language: Visual Basic .NET - Size: 22.5 MB - Last synced at: 8 days ago - Pushed at: almost 5 years ago - Stars: 4 - Forks: 2

hansiu/MatPhylobi

a tool for automatic construction of molecular data matrix for phylogenetic inference based on GenBank records

Language: Python - Size: 789 KB - Last synced at: almost 2 years ago - Pushed at: over 6 years ago - Stars: 4 - Forks: 0

dmyersturnbull/bioio Fork of PharmGKB/genome-sequence-io

Micro-libraries for reading and writing genomic sequence data in various formats.

Language: Java - Size: 690 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 0

lehwark/GBSON

A new annotation file format based on JSON, containing all information stored in the GenBank format but with advantageoius parsing and information structure properties.

Language: TypeScript - Size: 41 KB - Last synced at: 25 days ago - Pushed at: over 4 years ago - Stars: 3 - Forks: 0

vbaliga/genbank_downloadR

🔬 Batch downloading of DNA or protein sequences from GenBank

Language: R - Size: 104 KB - Last synced at: about 2 months ago - Pushed at: almost 5 years ago - Stars: 3 - Forks: 0

lucaspalmeira/bioinfo

Guia de programas e ferramentas de bioinformática e química computacional

Size: 16.6 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 2 - Forks: 0

RowanDurrant/BankIt_Checker

R function that checks .fasta files are suitable for GenBank submission

Language: R - Size: 9.77 KB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 2 - Forks: 0

dnanto/ffbio

flat-file sequence/database utils

Language: Python - Size: 606 KB - Last synced at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 0

oleon12/alignTools

Easy download and manage GenBank data, and alignments for phylogenetics

Language: R - Size: 747 KB - Last synced at: over 2 years ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 0

blackrim/phlawd_db_maker

this will just get the ncbi db from genbank made

Language: C++ - Size: 844 KB - Last synced at: over 2 years ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 2

Elliot-Chan-120/NCBI__NtDb_GenBank_Parser

Parses GenBank files from the NCBI nucleotide database using accession number and email address associated with NCBI account. Is capable of outputting a .txt file containing basic sequence information, source, CDS, and gene feature dictionaries as well as generate a linear gene map visualizing all of the aforementioned information.

Language: Python - Size: 25.4 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 1 - Forks: 0

mdcjansen/DBA

DNA barcoding analysis pipeline

Language: Python - Size: 16.7 MB - Last synced at: 5 months ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 1

gregyjames/GBtoTiny

Genbank to TinyDB.

Language: Python - Size: 498 KB - Last synced at: about 1 month ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

brinkmanlab/MicrobeDB

Curated mirror of RefSeq Microbial Genomes. Available via CVMFS repository.

Language: Shell - Size: 71.3 KB - Last synced at: almost 2 years ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 0

abhijeetsingh1704/PROTEINcleaner

a python utility to clean PROTEIN sequences and headers

Language: Python - Size: 6.84 KB - Last synced at: 4 months ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 0

loalon/gbcrawler

GenBank complete parser

Language: Python - Size: 1.9 MB - Last synced at: about 1 month ago - Pushed at: about 5 years ago - Stars: 1 - Forks: 0

ShawHahnLab/genbank-sub-20181109-dloop

GenBank Submission 2018/11/09

Language: Python - Size: 97.7 KB - Last synced at: over 2 years ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 0

ainefairbrother/GenBank-parser

This is a parser written to extract data from a GenBank file and insert it into an SQL database. This is part of a project that I did for my MSc in Bioinformatics.

Language: Python - Size: 12.7 KB - Last synced at: over 2 years ago - Pushed at: almost 7 years ago - Stars: 1 - Forks: 0

toddknutson/genbank_scrapper

GenBank Metadata Extraction Tool

Language: Python - Size: 1.43 MB - Last synced at: almost 2 years ago - Pushed at: about 8 years ago - Stars: 1 - Forks: 0

pseudogene/uniprime 📦

A workflow-based platform for improved Universal Primer design

Language: PHP - Size: 183 KB - Last synced at: 4 months ago - Pushed at: over 9 years ago - Stars: 1 - Forks: 1

spyisgooddawg/Genome

Genome is a platform for exploring and analyzing genetic data. Join us in advancing genomic research and collaboration! 🧬🌐

Size: 3.91 KB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 0 - Forks: 0

engkinandatama/NCBI-Sequence-Fetcher

NCBI Sequence Fetcher is a Python desktop app for downloading nucleotide sequences and extracting metadata from NCBI. It features an easy-to-use GUI, supports FASTA and GenBank formats, and helps researchers students and bioinformaticians efficiently collect DNA sequences and store metadata in Excel files.

Language: Python - Size: 26.4 KB - Last synced at: 2 days ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

ankushgpta2/tostadas Fork of CDCgov/tostadas

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

Language: Python - Size: 1.36 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

masikol/con-hi

The program annotates low-coverage and high-coverage regions of sequences in fasta format

Language: Python - Size: 209 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

boopsboops/ancistr

Automatically make an Ancistrus phylogeny and identify the common bristlenose catfish

Language: R - Size: 143 KB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 0 - Forks: 0

tomek7667/biotech-js

Package developed at A&A Biotechnology for reading all kinds of biotechnology related files

Language: Gnuplot - Size: 46 MB - Last synced at: 2 months ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

mansikath/Fasta-to-Genbank-Converter

A simple Python script using Biopython to convert FASTA files to GenBank format. The script prompts the user for input and output filenames, along with the molecule type (default is DNA). Ensure accurate and annotated GenBank files for your biological sequence data.

Language: Python - Size: 5.86 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0