ecoli_serotyping
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phac-nml
In silico prediction of E. coli serotype
First, I want to thank you for your work in this pipeline, but I have been trying to run ECTyper since yesterday without success and it seems to be a...
This PR adds support for reads compressed in gzip and bzip2 format; compression formats are auto-detected and compressed reads are decompressed to a temporary file for subsequent processing by the...
There is a talk and reference and diagnostic lab requests for adding O-antigen subtype information due to different phenotypic and clinical manifestations associated with these subtypes. The subtypes of interest...
* the [RefSeq sketch](https://gembox.cbcb.umd.edu/mash/refseq.genomes.k21s1000.msh) is stale and needs to be updated more frequently to match with the NCBI RefSeq database sketch. * Also in species prediction module implement species prediction...
Would be a fun task for anyone who wanted to try out Dataclasses: https://www.youtube.com/watch?v=T-TwcmT6Rcw. Can use the backport in 3.6 https://github.com/ericvsmith/dataclasses and just swap it out when we move to...
https://us.pycon.org/2018/schedule/presentation/162/ Currently available for py36 as a standalone and will be in stdlib for py37. There should be a backport somewhere for py27.
[eci_2792_genome_sequence.zip](https://github.com/phac-nml/ecoli_serotyping/files/1218728/eci_2792_genome_sequence.zip) For Stx1A gene (possibly others too, haven't checked), VF module reported two overlapping copies of this same gene at the same locus: e.g. Contig: https://www.github.com/superphy#00856f353e3710088ec7582e30ce8578bbeb43b1/contigs/lclECI-2792NODE_8_length_178059_cov_24.9142_ID_15 Copy1 start: 174082 Copy2...
Hello, I recommend to add in the instruction that -o argument is required. On my system without the output dir specified, I got the error "TypeError: unsupported operand type(s) for...
Currently version 1.0.0 of the tool only allows to type single culture/pure E.coli inputs. Since often biological inputs are contaminated, mixed culture or of metadata type, there is a growing...