bettercallsal v0.6.1

bettercallsal is published!

Read our article at Frontiers in Microbiology.

This is the v0.6.1 release of bettercallsal with following changes:

• NCBI datasets is updated to v15.3.1.
• Improved the stability of the bettercallsal_db workflow.
  • It is strongly recommended that you run the bettercallsal_db workflow in grid computing or similar cloud computing (Ex: aws batch) setting for the following reasons:
    • The second process of the workflow (FILTER_PDG_METADATA) spawns ~469 jobs to first query NCBI to fetch accessions for whom genome FASTA's are downloadable.
    • The penultimate process of the workflow (SCAFFOLD_GENOMES) also spawns >300 jobs to download the genome FASTA's and scaffold them.
  • Internal tests show that with stable internet connection, the bettercallsal_db workflow finishes in approximately 1 hour and 30 minutes.
• Fixed a bug wherein the creation of per_snp_cluster db was not retaining the genomes whose contig / scaffold sizes are identical per the waterfall algorithm.