Releases: FGPLab/cydrasil
Cydrasil version 3.0
This is our official 3.0 release, that coincides with a complete re-curation of the database to update all entries to the latest NCBI taxonomy as of May 2021, along with a complete new format for sequence IDs.
The re-curation led to the removal of 202 sequences. Many of these sequences were duplicate strain-level entries from single-cell sequencing projects in the Prochlorococcus, Synechococcus, and Microcystis genera. Sericytochormatia in the sibling clade group also had a large reduction, due to a change in the taxonomic definition of the group.
There was an addition of 47 new sequences.
From Cydrasil v3 onward, sequence IDs are now easily parsable using automated methods. Each sequence header is now defined by the database and corresponding database ID, followed by the current NCBI taxonomy.
Format as follows:
CY-sourceName-sourceDatabaseID#g__generaName.s__speciesName.str__strainName
Example
-----------------------------------------------------------------------
CY-IMG-641250527#g__Acaryochloris.s__marina.str__MBIC11017
CY-NCBI-AB112435.1#g__Acaryochloris.s__sp.str__Awaji-1
-----------------------------------------------------------------------
Finally, phylogenetic reconstruction has moved to RAxML-ng in order to both support the new sequence header format and to move to the current standard.
Cydrasil version 2.0
This is the next major update for the Cydrasil reference package and database. We expanded the Sibling Clade group to include 64 additional 16S rRNA gene sequences, while also taking further curation measures across the entire reference sequence collection.
This release also includes a JSON database file that has meta-data for every sequence in the reference package, including a link to the data source (or contact information if it was a user submission) and any warnings about the sequence.
We have also updated the recommended pipeline by including files needed to use SSU-Align (instead of PaPaRa) to align query sequences to the reference alignment, and have updated to use the new EPA-ng sequence placement program instead of the RAxML 8 implementation of EPA.
v1.0.1-zen
Release to sync with Zenodo for DOI. Issues with first release.