Recent Releases of ncov2019-ont-nf
ncov2019-ont-nf - 2.0.0
- [breaking change] This pipeline no longer does basecalling and barcoding inside the pipeline.
- Use Medaka by default instead of Nanopolish in artic
- Updated tools used by the pipeline
- Updated GISAID Excel template
- Python
Published by dialvarezs almost 3 years ago
ncov2019-ont-nf - 1.5
- Correctly handle variant when it has multiple words (e.g. "Probable Omicron").
- Moved pipeline own containers from DockerHub to GitHub Container Registry.
- Python
Published by dialvarezs over 4 years ago
ncov2019-ont-nf - 1.3
- Software updates
- Dropped GISAID clade assignment, and added "Variant" as a column in output file
- Now collects software versions
- Python
Published by dialvarezs almost 5 years ago
ncov2019-ont-nf - 1.2
Updated Nextclade and Pangolin
- Python
Published by dialvarezs about 5 years ago
ncov2019-ont-nf - 1.1
Simplified Guppy configuration
- Python
Published by dialvarezs about 5 years ago
ncov2019-ont-nf - 1.0
Initial version of the pipeline. Includes:
- Basecalling and demultiplexing using ONT Guppy (optional, requires Guppy previously installed)
- Assembly and variant calling using ARTIC
- Variant annotation using SnpEff
- Identification of clades/lineages of GISAID, Pangolin and Nexstrain
- Quality metrics and statistics (qc, coverage)
- Generating of final summary in Excel format containing relevant information obtained by the pipeline
- Inicial preparation for GISAID submission
- Python
Published by dialvarezs about 5 years ago