Releases · artic-network/artic-mpxv-illumina-nf

Add a modified align_trim (from fieldbioinformatics) for primer trimming and normalisation of read depth.
Move away from bbnorm for normalisation, resource utilisation is too high to be reasonable.
ivar trim was fine for sequence based primer trimming but it's simpler to do something that is alignment based
Add various primer schemes and move to the suffix based scheme naming system for scheme remaps
Remove variant annotation due to NCBI gff3 files being incompatible with bcftools csq
Add option to skip host filtering if desired

Assets 2

16 Sep 12:10

BioWilko

1.0.14

77bd8e2

artic-mpxv-illumina-nf v1.0.14

Changes:

Correct the name of the "erasmus" scheme to "Rigshospitalet" at request of scheme generators
Change primer scheme naming nomenclature to include a suffix. This follows the format of z.y.x-abc. Selecting the correct version is vital for wet lab work and bioinformatic analysis, full details below.

z.y.x-abc

z: represents a total resigned of a scheme.
y: represents a change in primers to an existing scheme. Ie adding spike in primers to account for new mutations.
x: represents a change in the primer concentration used. No change to the primer sequences.
-abc: an optional suffix to represent a scheme being remapped to a new reference genome. No changes to the primer sequences or concentration.