-
When using sff_extract (seq_crumbs 0.1.8) on SFF files that contain amplicon reads, I get the warning:
---
WARNING: weird sequences in file /srv/whitlam/bio/data/pyrotags/raw/Gasket67/Gasket67.sff…
-
accumulate papers describing oligotypes and amplicon sequences and exact sequence variants
-
Create:
* tables for the GTDB basis
* tables with association with the classification of OTUs and ASVs in the platform
* functions for classification of representative sequences for OTUs and ASVs (…
-
Hi,
Great tool for implementing L. pneumophila SBT! Thanks.
I'm trying to call SBT using nanopore sequenced multiplex PCR amplicons. However, I get "no product" results for some of the alleles. S…
-
[concatenate_read_example.pdf](https://github.com/willros/nanomux/files/15457608/concatenate_read_example.pdf)
Hi William,
How do you define where do the barcode starts and ends in the read?
I fo…
-
Hi there,
I have two questions:
1. You have mentioned that "ONTbarcoder has been optimized for protein coding gene like COI. While **there are ways** to obtain consensus for length variable non …
-
Hello! Thanks for putting together CliqueSNV - the ability to leverage long reads should be really powerful across different fields I think. I was curious if it would be possible to use long reads tha…
-
In some cases, a user might have sequenced an amplicon that is longer than the sequences in the database one wants to use. For this to work, ASV sequences could be cut before taxonomy assignment.
-
Inspired by @cassiawag's work on large deletions in ORF7/8 often masquerading as stretches of Ns in assemblies rather than as deletions, I had a look through currently submitted sequences to see if I …
-
core genes: 2017
single copy core genes: 1836
Number of conserved sequences: 1812
species specific conserved sequences: 536
potential primer pair(s): 4578
primer pairs with good target binding: 4…