coverage is added to the nucleotide csv file.

This release of MinVar includes an update to add coverage information for each site in

Added

• coverage information for each site is added to the merged_mutations_nt.csv file.

Ambiguity score is now computed on PRRT up to aa 335. Few bugfixes.

Changed

• Ambiguity score is now computed on PRRT up to aa 335.

Fixed

• Bugfix: unannotated mutations were not always reported in the tables (issue #25).
• Reference and consensus protein sequences having the same end would make annotate.py fail, fixed.

Predict resistance to HIV drugs, include ambiguous consensus

This release of MinVar includes several changes and a couple of important updates.

The most important is that, when running on HIV, sierrapy
is used to interrogate HIVdb and obtain prediction of resistance to drugs.

The report also includes ambiguity scores (fraction of ambiguous nucleotides), a measure useful to
estimate the time of infection.

Further, a consensus sequence with wobble bases is now part of the output.

Added

• Report now includes ambiguity score derived from ambiguous consensus sequence.
• Consensus sequence with ambiguous bases is saved into cns_ambiguous.fasta.
• Cells of drug resistance report are colour coded.
• The report includes levels of drug resistance inferred by HIVdb.

Changed

• Recombinant sequences are checked for also with HIV data.
• Threshold for sierra is read from the INI file ~/.minvar/runpars.ini
• Minor changes in final report.
• masterComments files with DRMs lists are updated to version 8.4
• Both full drug name and abbreviation are written.
• Subtype inference only reports top hit, subtype names are now clearer.

Many bug fixes (tested on dozens of samples)

• Date added on every page of the report, major mutations are in bold.
• Bugfix: minvar now works evene when neither HCV nor HIV reads are present.
• Bugfix: find_subtype failed when reads from both HIV and HCV were present.
• Bugfix: when no RAS mutation is found, reportdrm failed.
• Bugfix: when the frequency of a mutation is 0.5/0.5, cns_max_freq was longer than the reference.
• Problems with an assert when all reads have indels: removed the assert, phase_mutations has limitations.

Draft run information in the report

This small update adds some basic information to the report.

MinVar 2.1.1 fixes a sneaky bug

When sample consensus starts with a stop codon the whole numbering of the mutations was wrong.
This was discovered on a HCV sample.

Support for non-overlapping amplicons

MinVar now also works with non-overlapping amplicons.

With this update, the program takes the first and the last position that is covered by 20 reads at least. In the previous version, problems were observed on HIV that was sequenced with two non-overlapping amplicons.

For a similar reason also a drop in the coverage caused the premature end of variant calling. This was observed, for example, on HCV samples.

MinVar 2 has HCV support

MinVar has undergone a substantial restyling, but the most important feature is that HCV support has been added. Mutations are called with respect to H77 strain. There is no need to specify which organism is being analyzed, it is automatically detected.

The creation of consensus sequence is more robust, the program should run slightly faster (more tests are needed) and the final report is both better styled and more customizable (documentation will come soon).

Version 1.1: first minor release after paper version

No major features are added, but the function calls are now better orchestrated
so that one can easily turn off calibration. Moreover, documentation and
ansible instructions were added.

MinVar used in manuscript

This is considered a production version, tested on Illumina Miseq and Roche 454 data as reported in the manuscript (under review).