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Recent Releases of viper

viper - v2.3.1

Update README and CITATION.cff Full Changelog: https://github.com/Matthijnssenslab/ViPER/compare/v2.3...v2.3.1

- Python
Published by LanderDC over 1 year ago

viper - ViPER v2.3

  • Update the documentation on the classification feature (ab2a4583ffb9945d48676b4e78d4f86abd60e61c)
  • Improve error messages and the implementation of error checkpoints
  • fix minor bugs

Full Changelog: https://github.com/Matthijnssenslab/ViPER/compare/v2.2...v2.3

- Python
Published by LanderDC over 1 year ago

viper - ViPER v2.2

  1. Update software versions:
  2. geNomad 1.7.3 -> 1.8.0
  3. SPAdes 3.15.5 -> 4.0.0
  4. Clean Trimmomatic command for improved readibility
  5. Add name option to viper-classify.sh

Full Changelog: https://github.com/Matthijnssenslab/ViPER/compare/v2.1...v2.2

- Python
Published by LanderDC about 2 years ago

viper - ViPER v2.1

Changelog

  • general fixes
  • Improvement for Krona charts (sequences with no hits are also reported now)
  • improvements to viper_cluster_study (reinclude fasta is not required anymore and the clusters tsv file name now contains the coverage and identity cutoffs)

- Python
Published by LanderDC over 2 years ago

viper - ViPER v2

What's Changed

  • Per-sample clustering using geNomad for proviruses identification by @lisalenafaye in https://github.com/Matthijnssenslab/ViPER/pull/4
  • keep unclustered fasta file if no clustering possible by @lisalenafaye in https://github.com/Matthijnssenslab/ViPER/pull/5

New Contributors

  • @lisalenafaye made their first contribution in https://github.com/Matthijnssenslab/ViPER/pull/4

Full Changelog: https://github.com/Matthijnssenslab/ViPER/compare/v1.1...v2

- Python
Published by LanderDC over 2 years ago

viper - v1 CheckV proviruses

Development:

  • Per-sample and cross-sample clustering scripts with CheckV to find proviruses

- Python
Published by LanderDC almost 3 years ago

viper - ViPER v1.2.1

  • Also rename the scaffolds fasta and add the sample names to the NODEs

- Python
Published by LanderDC about 3 years ago

viper - ViPER v1.2

New updates: - Use contigs instead of scaffolds for final output - Change default blastn pid for clustering to (ANI for clustering - 5) - Improve info/error messages - fix bugs with unpaired reads and clustering - README updates

- Python
Published by LanderDC over 3 years ago

viper - ViPER v1.1

  • General updates
  • Set default options for --cluster-coverand --cluster-identityat 85 and 95, respectively.

New options: - You can use --keep-reads to keep the original read files in place and not move them anymore to the output directory. - Skip the trimming of reads for quality and adapters with --skip-trimming, useful if you already trimmed your reads with other software. -u | --unpaired can be used to optionally give an unpaired read file if you skip trimming. - -n | --name lets you specify a prefix for the output files.

- Python
Published by LanderDC over 4 years ago

viper - ViPER v1.0

First release of the ViPER scripts, used in the Laboratory of Viral Metagenomics (KU Leuven) to process paired-end Illumina reads from virally enriched samples. New releases will become available when certain dependencies have undergone major updates or when these scripts are altered.

- Python
Published by LanderDC almost 5 years ago