charlesfoster

Is there a way to disable output of alignments/gene extraction?

2

Hi, Thanks for the useful tool. I'd like to use nextclade_cli in a pipeline purely to get the `*..auspice.json` and `*.tsv` (clade assignment, QC etc.) files. I don't need the...

GetOrganelle with circular bacterial chromosomes/plasmids?

1

Hi, GetOrganelle works well for mitochondria and chloroplasts. Do you think it would for assembling bacterial chromosomes or bacterial plasmids?

Minimum depth threshold for "samtools coverage"?

3

#### Is your feature request related to a problem? Please specify. I'd like a simple way to calculate the coverage stats for a bam file. The closest out-of-the-box thing I...

Error with filter_by_abundance()

5

Hi, I'm running MitoZ through singularity after converting the docker container into an image (.sif). The pipeline runs well on some samples, but on 'weaker' samples with low abundance of...

mmseqs createtaxdb unexpectedly killed

1

I'm trying to use a clustered version of the NR database for taxonomy assignment but am running into some issues. Any assistance would be appreciated. ## Expected Behavior When running...

Segmentation fault at stage of joining output blocks

3

Hi, Thanks for the great tool. I've used `diamond` successfully to create a database using a version of the clustered NR database (https://osf.io/tejwd). I've outlined the steps I used to...

salmon taking unexpectedly long to map reads

4

**Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)?** salmon **Describe the bug** I'm working with 15 samples, with ~5Gb total reads per sample (90,000,000 to...

Pipeline erroring out because of problem with salmon index

5

### Description of the bug Hi, I have been having issues with `nf-core/rnaseq` erroring out at the `salmon` step. I've got a lengthy discussion over at the `salmon` github page...

Issues with final genbank-format file

4

Hi, Thanks for the interesting tool. I've tried it out on a de novo assembly of an RSV isolate, but the resulting genbank-format file is incomplete with some minor errors....

Ready to replace lofreq2?

1

Hi, This issue isn't really an issue per se, but more a question about the status of `lofreq3`. I use `lofreq` version: 2.1.5 in an analysis pipeline for SARS-CoV-2. I...