platon

This is a minor update introducing several technical improvements under the hood:

• Introduced a new --meta option to run Platon's internal gene prediction in metagenome mode: https://github.com/oschwengers/platon/commit/78747e89c80daaad54391ff457fad748aa9acd96
• Updated 3rd party dependency versions and checks: https://github.com/oschwengers/platon/commit/8c2c09a70c59ddca6a00c9d8f34868ea63d8c92b https://github.com/oschwengers/platon/commit/63aed6fbc75c7ebe258e68cce6241808135e809f https://github.com/oschwengers/platon/commit/5e4c12621c6f46379cfd1078b75256cbdfdb4f19 https://github.com/oschwengers/platon/commit/4a23c2788a1a176d4a1d17a21a87d8090b9a74a7 https://github.com/oschwengers/platon/commit/a231648e3cee79e20446c3b8f4de65c6eedc64a7
• Prevented Blast from phoning home: https://github.com/oschwengers/platon/commit/f61492e363c2fe22229b477b938e94374bf7aa3d
• Introduced auxiliary scripts to collect further information: https://github.com/oschwengers/platon/commit/2c74fd86d94d643a7bf3d79cd07b2d5d5b5e1d37

In addition we

• amended output files and messages: https://github.com/oschwengers/platon/issues/38 https://github.com/oschwengers/platon/commit/b380964bb57f22060c1b30118ece1727687ce852
• updated and fixed the readme
• updated and fixed CI scripts

This is a minor update introducing several technical improvements under the hood:

• bumped several 3rd party dependency versions
• added & improved CI tests
• source code modularizations
• Python3 code refactoring

In addition we

• adjusted the mobilization detection evalue to 1E-10
• discarded bundled 3rd party dependencies in favour of using conda or manually installed executables

This is a minor release updating the database:

A new database is built upon RefSeq 202 database release 202 containing complete:

• 20,041 chromosomes
• 18,795 plasmids

Now, circularity and coverage information can be parsed from Unicycler assembly fasta headers.
Several fixes and improvements were applied to the MPS creation process related to the UniRef90 seed sequences

This is a minor version update introducing:

• a new --prefix option

and fixing two bugs:

• catching occasional empty output of Prodigal
• executing Prodigal in meta mode on small sequences (characterizations of single contigs/plasmids)

This is a patch release fixing the following bugs:

• reactivate inc group detection
• replace nucmer by a single core compiled version
• adapt inc group output

This minor release introduces a new --mode parameter to choose from 3 distinct contig filtering modes:

• sensitivity: only applies sensitivity RDS threshold (-7.7) - actually more like excluding chromosomal contigs.
• accuracy (default): applies sensitivity & specificity thresholds as well as characterization heuristics
• specificity: only applies specificity RDS threshold (0.4)

This is a minor release fixing a Diamond bug under MacOSX.

This is a major update on the latest release.

In this release we introduce UniProt's UniRef90 protein clusters which replaced the NCBI's PCLA prokaryote clusters. Furthermore, we substantially revised and improved the RDS formula of the RDS metric and added new contig characterizations. Also Platon now takes advantage of the manually curated relaxase HMM profiles of MacSyFinder.

In detail:

• enhanced formula for the RDS calculation
• enlarged MPS db size (~4.1 mio) due to a switch to UniProt's UniRef90 protein clusters
• incorporation of MacSyFinder 's ralaxase HMM profiles
• implementation of an oriT detection by incorporating MOB-suite 's oriT sequences
• updates of all databaes
• many tiny bug fixes and improvements

The current database is available at Zenodo: https://zenodo.org/record/3751774 10.5281/zenodo.3349651

First update to v1.1.0.

• enhanced prediction performance by calibrated RDS
• updated Database to RefSeq release 95
• added Database checks

Database is available at Zenodo: DOI 10.5281/zenodo.3349651