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EBI-Metagenomics / mobilome-annotation-pipeline

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Virify debug, user_mobilome_clean output added, and amrfinderplus report improved #31

Closed Ales-ibt closed 4 months ago

Ales-ibt commented 4 months ago

VIRify viral predictions debug. Missing predictions are now visible in the final GFF file

The user_mobilome_clean.gff output is now generated and includes an extra key in the attributes column to label the type of MGE to which the CDS belongs.

AMRfinderplus report improvement. This is what it looks like now:

gene_id contig_id   gene_start  gene_end    ref_coverage    ref_identity    class_summary   ref_gene_name   ref_sequence_name   location
GNBBHOPO_00175  ERZ13633678.1-NODE-1-length-230215-cov-8.265911 182476  183627  100.00  100.00  AMR|AMR|EFFLUX|EFFLUX   mexA    multidrug efflux RND transporter periplasmic adaptor subunit MexA   chromosome
NA  ERZ13633678.18-NODE-18-length-106543-cov-7.185880   3   275 63.19   100.00  STRESS|METAL|MERCURY|MERCURY    merR    mercury resistance transcriptional regulator MerR   mobilome:plasmid
GNBBHOPO_02489  ERZ13633678.18-NODE-18-length-106543-cov-7.185880   347 697 100.00  100.00  STRESS|METAL|MERCURY|MERCURY    merT    mercuric transport protein MerT mobilome:plasmid
GNBBHOPO_02490  ERZ13633678.18-NODE-18-length-106543-cov-7.185880   711 986 100.00  100.00  STRESS|METAL|MERCURY|MERCURY    merP    mercury resistance system periplasmic binding protein MerP  mobilome:plasmid
GNBBHOPO_02491  ERZ13633678.18-NODE-18-length-106543-cov-7.185880   1174    2883    100.00  98.95   STRESS|METAL|MERCURY|MERCURY    merA    mercury(II) reductase   mobilome:plasmid
GNBBHOPO_02492  ERZ13633678.18-NODE-18-length-106543-cov-7.185880   2919    3572    100.00  100.00  STRESS|METAL|MERCURY|PHENYLMERCURY  merG    phenylmercury resistance protein MerG   mobilome:plasmid
GNBBHOPO_02493  ERZ13633678.18-NODE-18-length-106543-cov-7.185880   3653    4291    100.00  99.53   STRESS|METAL|MERCURY|ORGANOMERCURY  merB    organomercurial lyase MerB  mobilome:plasmid
GNBBHOPO_02495  ERZ13633678.18-NODE-18-length-106543-cov-7.185880   5269    5703    100.00  100.00  STRESS|METAL|MERCURY|MERCURY    merR    mercury resistance transcriptional regulator MerR   mobilome:plasmid
GNBBHOPO_02497  ERZ13633678.18-NODE-18-length-106543-cov-7.185880   6001    6639    100.00  100.00  STRESS|METAL|MERCURY|ORGANOMERCURY  merB    organomercurial lyase MerB  mobilome:plasmid
GNBBHOPO_02498  ERZ13633678.18-NODE-18-length-106543-cov-7.185880   6751    7116    100.00  100.00  STRESS|METAL|MERCURY|MERCURY    merD    mercury resistance co-regulator MerD    mobilome:plasmid
GNBBHOPO_02499  ERZ13633678.18-NODE-18-length-106543-cov-7.185880   7113    7349    98.72   85.71   STRESS|METAL|MERCURY|MERCURY    merE    broad-spectrum mercury transporter MerE mobilome:plasmid
GNBBHOPO_04276  ERZ13633678.41-NODE-41-length-61116-cov-8.431912    41031   41819   100.00  100.00  AMR|AMR|BETA-LACTAM|BETA-LACTAM blaOXA-488  OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-488  chromosome
Ales-ibt commented 4 months ago

The most updated version of dev branch is currently available in codon.