b-ummi / den-im Goto Github PK

Hi Developers

Thanks for developing such wonderful pipeline. I saw that ViPR is now BV-BRC and have more DENV sequences 5477 genomes with 138 genomes being added (and with strain type since 2019-2022). Do you have plans to update the database? Also, will you suggest using the Asian tiger Mosquito and Yellow Fever Mosquito assemblies as well?

Request for Enhancement

We have a test MiSeq run and I observe loosing a lot of reads at trimming step. Is there a way to skip trimming and if user wish to give trimmed data as an input?

Besides I am confused regarding different type of coverage being reported by DEN-IM like integrity_coverage_1_1 and check_coverage_1_6

Hello, I encountered this problem when I entered the code. Is the file damaged?
N E X T F L O W ~ version 21.04.3
Not a valid project name: DEN-IM.nf

It's being deprecated from nextflow and causes nothing but mess!

Hello,

we have Dengue sequences (POLY gene) analysed by Sanger sequencing. Is it possible to feed in these fasta files into your pipeline, omitting the NGS part of the analysis?

Best wishes,

Thorsten