susCovONT v1.0.3

Updates in v1.0.3:

Added option for V3 or V4 primer schemes, default is now V4
Updated nextclade
Fix output report

susCovONT v1.0.2

Update in v1.0.2:

• Guppy basecalling and demultiplexing are performed in one command rather than two separate, as this gives the same file structure as basecalling/demultiplexing on the GridION

susCovONT v1.0.1

A couple of updates in this version after suggestions from users:

Run report and QC:

• Previously, QC_status = WARN for any sample where nextclade reported "bad"
• QC_status will now also report WARN for any sample with 90-97% confidently called reads
• The requirement of longest_no_N_run > 10 000 has been changed to a recommendation, and samples with longest_no_N_run < 10 000 will get QC_status WARN instead of FAIL

Run options

• Added option to change normalise value for a run with the argument --normalise (default is --normalise 500 )
• Added option to re-run samples with 90-97% confidently called reads using --normalise 0 (i.e. no normalising) to try to improve coverage.

susCovONT v1.0.0

The first release of susCovONT!

• In summary, this tool takes as input ONT sequencing data and outputs consensus fastas (using artic minion), qc (pct coverage ++), pangolin and nextclade lineages
• QC thresholds: >97% of bases must be confidently called (>=20X per base) and there must be a stretch of >10Kb seq without Ns