plasmidID
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BU-ISCIII
PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification.
Hi, I installed plasmidID using bioconda in a separate conda environment and I tried to run it using the below command in which I supplied file names with their directory...
Hi, thanks for plasmidid, a very useful tool. I encountered a problem when sample names contain a `.` The program crashes and returns the following error messages: ``` ERROR in...
please update the the docker run parameter, the docker executable: plasmidID.sh not plasmidID docker run -v $PWD:$PWD -w $PWD buisciii/plasmidid plasmidID.sh \ -1 test/KPN_TEST_R1.fastq.gz \ -2 test/KPN_TEST_R2.fastq.gz \ -d test/plasmids_TEST_database.fasta...
Hello, When executing the test script as in ``` $ PATH=$PATH:/home/moeller/git/med-team/mmmulti/plasmidid/bin TEST_DATA/test.sh || true Executing:../plasmidID -1 KPN_TEST_R1.fastq.gz -2 KPN_TEST_R2.fastq.gz -d plasmids_TEST_database.fasta -c contigs_KPN_TEST.fasta -s KPN --no-trim Forward reads: KPN_TEST_R1.fastq.gz Reverse...
I'm trying to run PlasmidID via the Bioconda release, and Am running into an issue with Pandas. Might be user error though! ``` CREATING SUMMARY REPORT (Thu Jun 30 01:24:20...
Hi there and thank you for this amazing tool! However, I found that sometimes some contigs are added to the "joined" fasta although they are not mentioned in the results.html....
Sometimes, mapping founds a plasmid, but then BLAST doesn't find any contig matching the plasmid to generate the summary, and plasmidID crushes with: ```bash CREATING SUMMARY REPORT (Fri Jul 12...
### PR Description Updated `summary_to_tab_group` in `summary_report_pid.py` to generate a second report where plasmid identification results are organized `per sample`. **Reasoning:** The previous implementation did not provide plasmid identification results...
