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# Bactopia v2 Overview
With tremendous effort by @mxrcon and @abhi18av, the [foundation for migrating Bactopia to DSL2 has been laid out](https://github.com/bactopia/bactopia/pull/228). This transiti…
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I'm a researcher interested in reading deeper about susieR, especially the part of with summary statistics based on Zhu's paper. I saw that in the paper of susieR you used it for fine-mapping, but is …
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I am running EDTA on a 1 Gb bird genome but it has not gotten past the TIR-learner step after 7 days. I am using the bioconda version 1.9.6. My command is:
singularity exec --cleanenv /cvmfs/singu…
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Hello,
I'm following the tutorial here: "https://bactopia.github.io/tutorial/" on a linux cluster (CentOS 6.10).
**Here is the buildb_custom.sh used in the conda environment:**
#!/usr/bin/env bas…
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Hi, I have tried to use pilon using the following command :
` java -jar pilon-1.21.jar --genome '/media/loutre/SUZUKII/assembly/merged/3-suzukii-polished-80-merged-renamed.fasta' --frags '/media/l…
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Hello
I have an error using delly. When I try to run the CNV Germline, I have an error: Segmentation fault (core dumped). I don't think that it is an installation error because I use the docker ve…
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When I followed step 5 (imputation and phasing on whole genome), segmentation fault happens when imputing chromosome 1 with reference genome of hg38:
Parameters:
* Seed : 15052011
* #Th…
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**Version info**
- bcbio version (`bcbio_nextgen.py --version`): 1.2.4
- OS name and version (`lsb_release -ds`): CentOS Linux release 7.8.2003 (Core)
**To Reproduce**
Exact bcbio command you ha…
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Dear @hasindu2008
This is a feature request.
Having set up my fast5-indexes and BAM file, I have realized that I sometimes want to run the analyses across specific contigs (up to 20-30 thousand…
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I think this will become more important once we have for example JBrowse desktop. Users should be able to open a plain text gff without having to open e.g. tabix, genome tools to sort it, etc (those a…