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Hi again
Thanks for fixing https://github.com/chapmanb/bcbio-nextgen/issues/1218 . Running the bcbio_setup_genome without a gff3 file now works fine. A new problem however emerged when adding the gf…
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Hi
I have bacterial genome which is hybrid assembled with both short and long reads. The assembly quality is pretty high. Now I want to call SNPs for association analysis, can I use my hybrid ass…
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**Submitting author:** @akrinos (Arianna Krinos)
**Repository:** https://github.com/AlexanderLabWHOI/EUKulele
**Version:** v1.0.2b
**Editor:** @will-rowe
**Reviewer:** @johanneswerner, @jcmcnch
**Arch…
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We need to write an explicit gff3 specification for our transcriptome gff3, with code to test this added to `check_gff_fasta.py`. Making transcriptome annotations compatible is the key to bringing in …
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Branching from issue #135. On top of AMR genes, scanning for virulence factors present in environmental bacteria would also be interesting.
TODO: virulence factor database needs to be curated to re…
bfjia updated
4 years ago
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hi, sorry to disturb you. I have met some problem when using gtdbtk to classify bins. here is the details
the code is: gtdbtk classify_wf --cpus 24 -x fa --genome_dir temp/binning/bin_refinment_maxbi…
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Hi,
I regularly run bacterial composition analysis using UniFrac distances based on the relative abundances returned by MetaPhlAn. The UniFrac algorithm requires a phylogenetic tree describing the …
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I have run the following command and got an issue. How can I solve it?
$ '/home/genomic-lab/anaconda3/envs/pyppi/bin/run_gubbins.py' -p gubbins clean.full.aln
--- Gubbins 2.4.1 ---
Crouch…
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Hello,
I want to do exploratory testing on all core genes of a bacterial genome set with aBSREL. Unfortunately my genomes are not very diverse so that I am left with only somewhere between 3 to 7 u…
iss89 updated
4 years ago
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Hi
I try to build a phylogenetic tree for 200 bacterial genomes based on 6 housekeeping genes. Here are the steps I used:
First, I aligned each single gene, delete gaps;
second, I concatenate si…