Tassy J. Bazile

Try to rename the BDDIR appropriately based on your genomic library of interest (e.g vertebrate_marmalian_db). Also, follow the three steps for building a DB (https://hpc.nih.gov/apps/KrakenUniq.html) Hope it helps.

Hi Robert, Is there any update regarding ONT reads? I'm processing some metagenomic samples that were sequenced through ONT. Each time I run bactopia the only output file generated is...

Hi Robert, I have been trying the run bactopia on hydrid samples from illumina and minION All the samples are in the directory fastqs_hybrid ( 2 SE samples , and...

Your point really makes sense. So, does bactopia allow that - polishing after the assembly? Indeed, my goal is the compare the results between hybrid and homogeneous assemblies. That's why...

I welcome, the recommendation. Part of work will be assembling a complete or near-complete genomes for the organisms I am working on. So, when we do hydrid, does polishing become...

Oh, yes! This kind of hybridization (long read first, polish with short reads) sounds interesting. We are getting more and more long reads to process. I appreciated you getting back...

Hi Robert, When you run bactopia on one hydrid sample ( mysample.fastq and mysample_1.fastq, mysample_2.fastq). How many output directories to expect? - I imagine just one ( bactopia_output/mysample) - But...

In the documentation, I notice we can run bactopia on assembly files (.fasta). Is it a good idea to run bactopia with the assembly files(in the assembly sub-directory) generated by...

Hi Robert, Is there any update about running bactopia on assembly files? I ran bactopia to process some local .fasta files, but had no output. The error log file is...

Hey Robert, bactopia --version bactopia 2.1.1 It has worked then! Prior to running bactopia datasets, I ran this conda install -c conda-forge -c bioconda bactopia Thanks!