NGSpeciesID
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ksahlin
Reference-free clustering and consensus forming of long-read amplicon sequencing
every time my instance of NGSspeciesID runs, it will never finish the medakka polishing 2 consensus formed. Saving spoa references to files: 945021|NC_016052.1/consensus_reference_X.fasta running medaka on spoa reference 3 using...
Hi there! I am trying to use NGSpeciesID with some custom parameters but I am not sure if maybe I am doing something wrong... here my command: `NGSpeciesID --consensus --t...
Hi, this is the error log for building parasail. For some reason, version.sh cannot be executed, I'm already running it with sudo. My system is Ubuntu 20.04.2 LTS. ``` (NGSpeciesID)...
Hi, I have been using NGSpeciesID on a microbiome dataset with 90 samples (one fastq file per sample). I use a for loop to loop through these samples with the...
Hello Kristoffer, I ran `NGSpeciesID` with the following command: ``` for file in *.fastq; do NGSpeciesID --t 4 --ont --fastq $file \ --consensus --medaka \ --abundance_ratio 0.005 \ --rc_identity_threshold 0.85...
Hi, We really would like to test and use your program, but we encounter some problems with installing it. It seems like the same problem that 2tony2 mentioned. So we...
I'm looking at the output from the pipeline and referring to text on the main page : "The final cluster information is given in a tsv file final_clusters.tsv present in...
Is there a way to adjust clustering parameters? for example, some OTU pipelines will generate different number of bins depending on whether you want 98% or 95% similarity clusters. I...
Dear Developers, I have tried multiple ways to install these packages. They all install fine independently (by installing them directly onto conda), but in an environment with python 3.6 specified,...
