dnasko/refseq_rollback

A collection of scripts to recreate historical RefSeq versions

RefSeq Rollback

A collection of scripts to create historical RefSeq versions.

Downloading the necessary files

The two files you'll need to rollback to a desired RefSeq version are:

1. The current bacterial RefSeq FASTA file
2. The catalog file associated with the version you want to rollback to.

Two scripts are provided to help you download these files:

./download_latest_bacterial_refseq.sh

./download_refseq_catalog.sh 80

download_latest_bacterial_refseq.sh will create a directory and download the latest bacterial RefSeq FASTA files, concatenate them and delete the pieces. download_refseq_catalog.sh will download the catalog file you want to rollback to, in the example we chose 80, though any version can be selected.

Rolling back to a desired RefSeq version

If you want to use these files to roll back to version 80, you would do the following:

./refseq_rollback.pl -catalog RefSeq-release80.catalog.gz \
		     -fasta RefSeq-release88.fasta.gz \
		     -out RefSeq-release80.fasta

Diversity calculations

In the MetaDB manuscript we present diversity metrics for bacterial RefSeq over time. The script used to create the OTU table in the analysis is create_otu_table.pl.

Rev DJN 10Jul2018