genbank

Scripts to download genomes from the NCBI FTP servers

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

A Go package for engineering organisms.

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

GET_HOMOLOGUES: a versatile software package for pan-genome analysis

Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy

Cenote-Taker2: Discover and Annotate Divergent Viral Contigs

VAPiD: Viral Annotation and Identification Pipeline

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.

An example GenBank file reader in Rust

😴 📂 Create and Query a Local Copy of GenBank in R

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.

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

all-in-one solution for discovering novel DNA barcode

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

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

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

Divergent Virus & Mobile Element Genome Annotation Pipeline

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.

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

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

LAVA: Longitudinal Analysis of Viral Alleles

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

Perl script to convert GenBank records to FASTA format

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

Parser (unofficial) for ncbi GenBank data

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

🔬 Batch downloading of DNA or protein sequences from GenBank