0.11.3

• first length-filter the input reads and then classify with kraken2
  • before, reads were length-filtered but the raw reads were classified with kraken2, leading to classifications of primer-dimers and other too sort (or too long) reads that are anyway not further used in the following steps of the pipeline

Attention: If you have for example a high proportion of short reads in your sample that are sorted out be --minLength, their classification as SARS-CoV-2, human or unknown will not reflect them anymore.

small fix to nanopolish output

• small fix to nanopolish output

0.11.1 VarSkip primer support

• support added for NEB varskip primer here
• activate via --primerV VarSkipV1a see also --help for all supported schemes
• example command:

nextflow run replikation/poreCov -r 0.11.1 --fastq_pass fastq_pass/  --primerV VarSkipV1a --update -profile local,docker

• default for the amplicon inclusions:

Min read-length set to: 350 [--minLength]
Max read-length set to: 700 [--maxLength]

0.11.0

Release 0.11.0

polishing models for guppy 5.x

• important guppy (for basecalling) / medaka (for genome polishing) model settings are both set default to high accuracy (hac)
  • make sure that you are using the correct models
  • if you basecall on a gridion or minion with hac settings the default medaka_model is fine if you are using guppy version 5 or higher (make sure to update minknow software)

    guppy_model = 'dna_r9.4.1_450bps_hac.cfg'
    medaka_model = 'r941_min_hac_g507'

• alternatively you could use nanopolish to avoid the whole model stuff (needs the fast5 data for polishing)

Additions and fixes

• --update now downloads the latest available pangolin AND nextclade container
  • for both the tool version and the database data are mentioned in the final report
  • this ensures that you can run porecov always with the latest available lineage and clade definitions
• fixed some errors by downloading databases via wget (https certificates) should be now future proof
• --sample input now checks if headers are present and if all fields are present (barcodes and sample names)
  • Please make sure that you are not using excel to generate the input csv use node pad, text-editor etc., any program that is not introducing strange hidden symbols.
• V4 primer support included (--primerV V4)
• fixed some bugs for CoVarplots
• medaka models for polishing are now pre-downloaded for the container
• --min_depth parameter (default 20) added, can be used for low depth genomes ( with only a few reads)
  • will be bad quality genomes but is usually enough to roughly determine the lineage it is from

0.10.3

Add V4 primer-pair output to the repair script for low coverage regions and amplicon drops.

0.10.2

Added support for slightly differently named coverage depth files for V4 primers to be used w/ CoVarplot

0.10.1 Add support for all available medaka models

After installation, medaka only comes with a bunch of most recent default models. Further (e.g. older) models are downloaded automatically the first time they are requested which can make issues on systems that have restricted internet access.

• added a new container for the ARTIC pipeline that has pre-downloaded medaka models

guppy 5.x support and min depth parameter inclusion

• added --min_depth parameter (default 20)
  • this is the minimum depth required for each nucleotide to not be masked to "N"
• updated to newest medaka version to support guppy 5.x models
  • default medaka model is now r941_min_sup_g507
  • Please change accordingly via --medaka_model (e.g. r941_min_hac_g507 or r941_min_fast_g507)

This is a pre-release and it might contain some bugs

vbz compression support

• vbz compression support added

bug fix on nanopolish

• Fixed a small bug that failed the pipeline via nanopolish and the coverage plot
• thx @iferres