This post explains what needs to take place to import an already manually curated genome into ggKbase. How to curate a genome: https://ggkbase-help.berkeley.edu/how-to/genome-curation/ How to curate many genomes: https://ggkbase-help.berkeley.edu/how-to/bulk-genome-curation/ Step 1: Rename Fasta File Make your curated genome distinct from the original organism in ggKbase by adding “_curated” or “_genome_final” to the end of the basename. Likewise,…
A guide to genome curation outside of ggkbase. Do you have MANY genomes to curate? See https://ggkbase-help.berkeley.edu/how-to/bulk-genome-curation/ Wondering how to get your already curated fa-file of a genome back into ggkbase? See https://ggkbase-help.berkeley.edu/overview/data-preparation-curated-genome/ Fix scaffolding errors with ra2.py First fix scaffolding errors in the genome (*.fa) downloaded from ggkbase using ra2. So what does ra2…
See http://ggkbase-help.berkeley.edu/how-to/genome-curation/ and https://ggkbase-help.berkeley.edu/overview/data-preparation-curated-genome/ for more thorough instructions on the steps. Overview Run ra2 on each genome. Run prodigal on each genome using the -single setting. https://ggkbase-help.berkeley.edu/overview/data-preparation-curated-genome/ Concatenate all files (fa, fa.genes, fa.genes.faa, fa.genes.fna), run 16s, trnascan, usearch, clean.rb, anno-lookup etc using concatenated files. Use break_bulk_bin.rb to unshuffle genomes – see below for specifics Submitting to ggkbase – see…
A post by Lin-Xing Chen, Karthik Anantharaman, Alon Shaiber, A. Murat Eren, and Jillian F. Banfield. For any questions about the methods described below, please contact us via email (linxingchen@berkeley.edu). Introduction The purpose of this post is to describe step-by-step procedure for scaffold extension and gap closing to dramatically improve the quality of metagenome-assembled genomes…