Scripts to download genomes from the NCBI FTP servers

A Go package for engineering organisms.

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

A genome visualization python package for comparative genomics

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

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

GET_HOMOLOGUES: a versatile software package for pan-genome analysis

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

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

VAPiD: Viral Annotation and Identification Pipeline

Nextstrain build for mpox virus

An example GenBank file reader in Rust

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.

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.

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

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

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

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

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

F# library for accessing and manipulating bioinformatic datasets.