v3.2

Add Nextera adapters
Ignore samples with more than 2 fastq files
Uniformization of warnings report
Make trueCoverage executable
Add trueCoverage references sequences for other species
Fix minor bugs
Add warnings to Trimmomatic when no reads survived the cleaning step
PASS, FAIL, WARNING rules (FAIL overrides WARNING):

• FAIL
  • Low estimated coverage calculated in EstimatedCoverage module (number of sequenced nucleotides / expected genome size) (default 15x). STOPs sample running.
  • Lower sample coverage, higher number of absent genes or higher number of genes with multiple alleles than specified in TrueCoverage module config file. STOPs sample running.
  • Fail FastQC “Per base sequence quality”, “Overrepresented sequences”, “Per sequence GC content” or “Sequence length distribution”. Do not pass FastQC “Per base N content” or “Adapter Content”. STOPs sample running if sample FastqQC fails after Trimmomatic reads cleaning.
  • AssemblyMapping module does not run successfully.
  • Assembly coverage (calculated in AssemblyMapping module) of filtered contigs does not reach the minimum required (30x).
  • MLST scheme found does not match with provided species (mlst module) (with the exception of Yersinia genus, which might raise a warning).
• WARNING
  • Fail FastQC “Per base sequence content”. Do not pass FastQC “Per base sequence quality” or “Overrepresented sequences”.
  • Zero read pairs survive Trimmomatic cleaning.
  • Higher number of contigs than allowed or odd number of assembled nucleotides.
  • Less than 95% of the reads mapped back to the assembly (in AssemblyMapping module).
  • mlst module did not run.
  • Found MLST scheme for a species with unknown scheme. In case of Yersinia genus, only raises a warning if the specific scheme found does not match with the scheme for provided species name (but matches the genus).