Changes for v0.02 - Githubissues

ammaraziz / ctgap

Chlamydia trachomatis Genome Assembly Pipeline

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Changes for v0.02 #1

Closed ammaraziz closed 8 months ago

ammaraziz commented 12 months ago

[x] Use scrubby for human removal step
[x] Filter for chlamydia spp
[x] Add fastp for adapter and quality trimming
[x] Collate coverage stats from samtools coverage, compute meanmapq for each genome hit.
[ ] get uniquely mapped reads for ct_ref.fasta alignment
[ ] use top hit reference for
- [ ] alignment based genome assembly
- [ ] denovo assembly
[x] replace spades with shovill
[ ] look at genome completeness for the alignment step

gokeson commented 12 months ago

Hurts my head, but that is what you do, isn't it? HAHAHAHAHA

gokeson commented 11 months ago

[ ] Use scrubby for human removal step

I can't seem to get scrubby installed via Conda. I have raised an issue on scrubby's GitHub page. Until the issue is resolved, I can do it manually by performing only kraken2 host reads extraction.

ammaraziz commented 11 months ago

See my comment on the github page about how to install scrubby.

get uniquely mapped reads for ct_ref.fasta alignment

Can you please create a unique set of references for this?

ammaraziz commented 11 months ago

It's okay if you want to test independent tools but we should aim to update the pipeline as we go along.

gokeson commented 11 months ago

See my comment on the github page about how to install scrubby.

get uniquely mapped reads for ct_ref.fasta alignment

Can you please create a unique set of references for this? Ct_refs.zip

I have got four representative genotypes here. I have some more work to do here on getting the best references to use for each body site but that will wait as it is part of another project that I am doing. Yes, the other project is comparing all Ct reference genomes and creating the best consensus sequence for each strain. For this I am using Illumina, nanopore to sequence all reference strains and then some historical 454 gap-closed genomes that the lab currently has.

For now, I think we can proceed with the four reference strains that I have included in the attached file as they are quite unique genotypes... quite different from each other (see below). 4RefComp

gokeson commented 11 months ago

[ ] replace spades with shovill I think, according to the documentation, shovill only works well on isolates. Most of the samples I envisaged this pipeline will be used for will be clinical samples which will most likely be metagenomes thus making shovill not very fit for purpose??

ammaraziz commented 8 months ago

Most of these have been completed or we've changed course.