Recent Releases of sphae
sphae -
- catches specific cases of having mutiple circular phages from nanopore assemblies
- updating the code to count the number of hypothetical proteins, and other genes with ambiguous annotations and classifies them as hypothetical
- Addressing issue#36- Phrogs annotated toxin not recognised in sphae summary output, now sphae summary checks for toxins too
- Sphae container added
- Python
Published by npbhavya over 1 year ago
sphae - v1.4.4
Two major changes: - adding the option to run pharokka with --pyrodigal-gv to test for alternate coding genes. To run the alternative gene prediction tool, change this in the config.yaml file - The phage plots in the final file were failing. This is fixed now
- Python
Published by npbhavya over 1 year ago
sphae - v1.4.3
Summary file update - missed adding DTR found or not when only one genome assembled per sample, added this in now - If recombinases or transposases are found, the genes are written to the summary. Also if AMR, virulence genes, CRSIPR spacers etc are found. - number of hypothetical proteins - total read length after QC and subsampling
- Updating the QC rule to touch the output file so the error is correctly recorded
- the annotate function table after the 3Ps weren't being generated, so I added that in
- updated phynteny yaml file to include numpy version
- updating the taxa description in the summary file to include the taxa description, lowest taxa and the isolated host from the pharokka inphared result
- added the --no-polish option for longreads, allows support for the new flowcells and pcbio sequencing
- Python
Published by npbhavya over 1 year ago
sphae - testing pypi workflow
Same as v1.3.3 but testing pypi github workflow
- Python
Published by npbhavya almost 2 years ago
sphae - sphae-v1.1.1
minor updates so the results folder has notes on where the sample failed.
- Python
Published by npbhavya over 2 years ago