bettercallsal v0.7.0

bettercallsal is published!

Read our article at Frontiers in Microbiology.

This is the v0.7.0 release of bettercallsal with following changes:

• Fixes SSL issue reported in #1.
• bettercallsal can now skip collecting hits (RefSeq or GenBank accessions) belonging to a NCBI BioProject. We have found that some genome assemblies had no corresponding run data submitted to NCBI (SRR's) and/or these genome assemblies were not up to internal quality metrics. We plan to incorporate additional genome quality filters in future releases.

  • By default, accessions belonging to BioProjects PRJNA766315,PRJNA675435,PRJNA831577,PRJNA855361 are ignored during mash screen step.

  • Use the --tuspy_skip command-line option to either turn this off or add more BioProject accessions:

    cpipes --pipeline bettercallsal --tuspy_skip false ...........

    or

    cpipes --pipeline bettercallsal --tuspy_skip 'PRJNA766315,PRJNA675435,PRJNA831577,PRJNA855361,PRJNA855362' ...........

• You can now turn off MultiQC report generation if the number of input samples is too big with --multiqc_run false command-line option.

All of our internal benchmark studies used the PDG000000002.2727 version of the NCBI Pathogens release for Salmonella enterica.

• You can download the pre-formatted database generated for PDG000000002.2727 with bettercallsal_db workflow from S3.