-
In the QIIME workflow, I am trying to replace the very slow and not appropriate vsearch classification of long-read metagenomics sequencing (ONT) by minimap2 which is very fast for this kind of reads.…
-
Hi,
I used following parameters for canu assembly:
```
canu -p wDi -d ALL_wDi_canu_seqtk45_CCS_1000_0.015_1000 genomeSize=1.5m correctedErrorRate=0.015 ovlMerThreshold=1000 batOptions="-eg 0.01 -eM…
-
When you run `bwa mem` etc each mapped read in given a mapping quality (MAPQ). In `bwa` a MAPQ=60 means it was uniquely mapped, and MAPQ=0 means it mapped to >1 location equally well.
What does Map…
-
I've been taking a look at the annotation sets that we currently import into the GOA database and that have been identified as being unmaintained, namely those from JCVI/TIGR and PAMGO_Mgrisea.
I'v…
-
It might be handy to have an estimation of the genome size (measured as the number of peptides) together with the peptidome clustering. This could help to spot false "complete genomes" that were initi…
-
## Version of Integron_Finder:
integron_finder version 1.5.1
Python 2.7.12 (default, Dec 4 2017, 14:50:18)
[GCC 5.4.0 20160609]
- open-source GPLv3,
- Jean Cury, Betrand Néron, Eduardo Ro…
-
Hi all, I'm a total novice at bioinformatics so please bear with me. I've been attempting a bacterial genome assembly with canu using nanopore reads. I submitted it to my uni hpc friday afternoon and…
-
I have RS II data and was wondering if there are parameter recommendations for bacterial genomes? I see recs for Sequel V2 on the FAQ but not RSII.
I ask because I ran Canu 1.9 with the default pa…
-
Hi,
I'm new to Github and wtdbg2. I have assembled a bacterial genome of size 6.3m using the command:
#!/bin/bash
/path/to/wtdbg2 -x ont -g 6.3m -t 16 -i /path/to/del_pobA_ICE_nanopore.fastq -fo…
-
Hello,
My run from before was able to finish but I just wanted to ask for some clarifications of some of the output files as I don't see anything in the README that specifically explains them.
W…