-
Hello Yu Peng,
The idba_ud tool is published by you.It is a so useful tool that I want use in my project.However,I got some problems in the process.
My command is "idba_ud -r 01_merge.fa --…
-
Hi,
I have created a db (canoncical) with 51mers. When i run query sequence of 51bp (25bp-SNP-25bp) it'll mostly return counts of 0. However if i lengthen those query sequences to 101bp(50bp-SNP-50…
-
Today I upgraded from lighter 1.0.7 to 1.1.1 and I first noticed a problem when 1.1.1 was outputting different number of reads in the two output files, and then noticed it was also passing far fewer r…
-
The idea would be, something like:
for node A, has attributes MIC_AMP_1: some number of genomes, MIC_AMP_2: some number of genomes.
We could do this after the fact to by going through the graph…
-
Hi,
I've been trying out m6anet on our RNA004 reads and I have a question about alignment. As a default, we tend to align our reads to the genome for isoform discovery. From what I noticed in the d…
-
Hi,
Thank you very much for such a nice tool. usage: PanGenie [options] -i -r -v
I fund the paper (https://www.biorxiv.org/content/10.1101/2020.11.11.378133v1)said that :we propose a new algor…
-
Dear Erik,
I am trying to GCSA index a graph from `edyeet`->`seqwish`->`smoothxg`->`vg view`->`vg prune -r`.
Input are 3 small genomes (2Tb) and practically does not finish.
I am not sure wh…
fbemm updated
4 years ago
-
Dear Dr. Wang, I met the following error when I trying to run SolidBin with my data. Would you give me any suggestions?
```shell
2021-01-10 20:38:16,017 - Input arguments:
16 2021-01-10 20:38:…
-
Re #7 : Consider adding read-level scores and thresholds. Possible scores:
- `kraken-filter` score: `taxon_kmers / unambiguous_kmers`
- [Andersen](https://bmcmicrobiol.biomedcentral.com/articles/…
-
Hello Team,
several questions related to omh and edit distance:
1. For edit distance in the edlib (https://github.com/Martinsos/edlib), there can be global, infix and prefix method (e.g., gaps op…