search

UPHL-BioNGS / Cecret

Reference-based consensus creation
MIT License
49 stars 26 forks source link

Adding MT903345 as mpx reference genome #342

Closed jl32587 closed 2 months ago

jl32587 commented 3 months ago

Our lab has been using MT903345.1 as reference genome (https://www.medrxiv.org/content/10.1101/2022.10.14.22280783v1.full) using older version of Cecret (v.3.4.20221121). The mpx_primalseq config now uses NC_063383.1. Is it necessary to set up a new profile using MT903345.1?

erinyoung commented 3 months ago

The bedfile coordinates have to match the reference sequence otherwise ivar trim or samtools ampliconclip can't figure out where the primers are.

Do you have a copy of the bedfile that you could share with me?

jl32587 commented 3 months ago

TX-DSHS_Mpx_bed.zip I have attached the reference fasta and bed files we are using. Thank you!

erinyoung commented 2 months ago

I DID NOT forget about this.

It's just that testing this takes a really long time.

I have added in new primer schemes that I have labeled mpx_yale into the latest updates that are currently going through testing.

If all goes well, this should get released by the end of the day. /fingerscrossed

To use these primers, you would set the params.primer_set = "mpx_yale" and params.species = "mpx" OR add mpx_yale to your profiles.

What command do you normally use? I can convert that to use these new values.

jl32587 commented 2 months ago

Thank you so much for working on this! The command I normally used is: nextflow run UPHL-BioNGS/Cecret --reads --outdir -profile singularity,mpx_primalseq

erinyoung commented 2 months ago

The new release is out!!!

I've named the profile that uses these primers the 'mpx_yale' profile. You should be able to run what you normally ran by updating the profile from mpx_primalseq to mpx_yale.

nextflow run UPHL-BioNGS/Cecret --reads <input_path> --outdir <output_path> -profile singularity,mpx_yale
jl32587 commented 2 months ago

Sweet! I'll test it on our dataset. Appreciate it!