Scripts to download genomes from the NCBI FTP servers

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

VAPiD: Viral Annotation and Identification Pipeline

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

An example GenBank file reader in Rust

Cenote-Taker2: Discover and Annotate Divergent Viral Contigs

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

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

all-in-one solution for discovering novel DNA barcode

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.

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

Divergent Virus & Mobile Element Genome Annotation Pipeline

LAVA: Longitudinal Analysis of Viral Alleles

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.

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

Parser (unofficial) for ncbi GenBank data

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

Perl script to convert GenBank records to FASTA format

🔬 Batch downloading of DNA or protein sequences from GenBank

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

this will just get the ncbi db from genbank made

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

Easy download and manage GenBank data, and alignments for phylogenetics

flat-file sequence/database utils

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

GenBank complete parser

GenBank Metadata Extraction Tool

A workflow-based platform for improved Universal Primer design