kinestetika/metaerg repository overview

⁠metaerg.2.5.10.

New to 2.5.10

• Now using minced instead of CRISPdetect for crispr detection
• Updated the blast database to GTDB 220, CDD to 3.21. The database now includes (113104, 189, 14447) taxa for (prokaryotes, eukaryotes and viruses) respectively.
• Fixed installation problems with some dependencies such as antismash, deepsig and some databases

New to 2.5

• Added the option to perform comparative genomics analyses for a group of related genomes
• Put contig nt fasta files of related genomes into a dir and run metaerg with --mode comparative_genomics.
• After regular annotation, protein sequences will be clustered with mmseqs and predictions will be made about shared gene context, degree of expression and the type of selection (purifying versus diversifying).

New to 2.4

• Minced, TMHMM and SignalP are no longer used as helper programs.
• CRISPRDetect, padloc, PureseqTM and deepsig are used instead.
• These changes reduce overall runtime.
• Various small bugs and inconveniences were fixed .
• Updated antismash to 7.1, diamond to 2.1.8
• If you have data previously annotated with metaerg, use --update_annotations to update.

New up to 2.3.41

• Updated to GTDB 214 and antismash 7.0
• Speed improvements
• Improved handling of the genetic code to better deal with genomes that have a different code
• Improved scalability: Metaerg can now annotate thousands of MAGs and millions of contigs (using --contig_mode)
• Now using sqlite for dynamic data storage during annotation, avoiding memory issues with very large datasets.
• Improved progress tracking avoiding needless work while re-running metaerg in case a run gets stopped.
• Curated and extended the hmm functional gene database, adding CRISPR-Cas systems, heme/copper oxidases, cytochrome bd oxidases, aminoacid biosynthesis, etc.
• Improved arbitration between repeat and open-reading-frame callers, leading to removal of more nonsensical ORFs and avoiding truncation of valid ORFs because of repeats. Note: This leads to a different numbering of genes and features compared to metaerg versions 2.2.X
• Metaerg now computes genome-wide codon-usage bias and estimates the growth rate of the associated organism. It also estimates which genes may be highly expressed (in addition to ribosomal proteins.
• Addition of new functional genes, refinement of functional gene calling, leading to fewer false positive and negative calls.
• Metaerg now creates an excel file with a table of all the identified functional genes for all genomes annotated.

⁠To install the databases at /path/to/database_dir; you need 165 Gb of disk space and you need write access to this dir:

docker run --network host -v /path/to/database_dir:/databases metaerg metaerg --database_dir /databases --download_database

⁠Then, to update the hmm functional gene database to the latest version:

docker run --network host -v /path/to/database_dir:/databases metaerg metaerg --database_dir /databases --create_database S

⁠To annotate one genome:

docker run --network host -v /path/to/database_dir:/databases -v /path/to/dir_with_fasta_file:/data metaerg metaerg --database_dir /databases --contig_file /data/fasta_file

⁠To annotate many genomes, each in a fasta file ending with .fa:

docker run --network host -v /path/to/database_dir:/databases -v /path/to/dir_with_fasta_files:/data metaerg metaerg --database_dir /databases --contig_file /data --file_extension .fa

⁠Use of this image on HPC:

To run the docker image on a HPC, as explained by jkzorz⁠:

singularity pull docker://kinestetika/metaerg
singularity run --bind path/to/metaerg/database:/databases  ~/metaerg_latest.sif --database_dir /databases --download_database
singularity run --bind path/to/metaerg/database:/databases --bind /path/to/dir/with/my/contig_fasta_file:/data  ~/metaerg_latest.sif --database_dir /databases --contig_file /data/contig_fasta_file
``
(with path/to/metaerg/database and /path/to/dir/with/my/contig_fasta_file pointing to the target dirs on your file system)

Or:

apptainer build metaerg.sif docker://kinestetika/metaerg:latest

===
Check out [metaerg on github](https://github.com/kinestetika/MetaErg) for more information.