CRISPRCasTyper

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ValueError: invalid literal for int() with base 10: 'lengt'

2

Hello. I first ran the single bins(2159kb) and he was able to output the results properly, but when I merged the 1472 bins (3.39Gb)into one fasta file and ran it...

AndAvia

(Question) provide GFF file for pre computed gene calls?

5

Let's say you already ran prodigal and/or have gene calls in GFF format, can you skip the prodigal run and provide the GFF file? antiSMASH provides a similar option since...

jolespin

.. xgboost will fail with a "Incompatible model" error. This should be handled more gracefully

Russel88

Russel88

Execution against protein fasta and gff

2

Hi, First of all, I would like to thank you for developing this wonderful tool. My question is about the input files of the tool. Currently I have a genome...

xvtyzn

castyping.py having an issue with positional arguments.

2

I've had cctyper working before on another machine. Not sure if you have seen this error before. (cctyper)user assembly % cctype CIA1\ copy.fna CIA1_cctyper zsh: command not found: cctype (cctyper)user...

jamesrgurney

Creating empty files when there's no data

1

Hello, First of all, fantastic software! I've been trying it out and it's super cool. I have a suggestion regarding the output files. As you mention in the README: _files...

nataquinones

alternative to minced?

1

Thanks for the great tool! In some cases it might be nice to be able to use CRISPR repeat/spacer arrays identified using a different tool or identified previously. For example...

ltcall

At the moment, low-quality single-effector HMM matches near a CRISPR is only visible in the plot, but are not included in the CRISPR_Cas_putatitive.tab output file. This should be fixed.

Russel88

Include HMMs for fusion proteins, such as Cas1-RT, Cas4-Cas1, and Cas6-RT-Cas1

Russel88