ECTyper IRIDA plugin version 2.0.0

IRIDA plugin that fully supports ECTYPER v2.0.0 and can be installed together with other ECTYPER plugin versions including v1.0.0 and 1.0.0b

Full Changelog: 1.0.0b...v2.0.0

ECTyper IRIDA plugin version 1.0.0b with IRIDA v21.01 support

• Identical to version 1.0.0 with IRIDA v21.01 full compatibility (Issue #1)

ECTyper IRIDA plugin version 1.0.0

IRIDA plugin for ECTyper version 1.0.0 supporting new features such as

• QC status
• Database version
• Adjusted O and H antigen thresholds allowing to re-run samples at more relaxed conditions in case no call is obtained for a given antigen
• %identity and %coverages for antigen genes are reported now

IRIDA wrapper for ECTyper version 0.9.0

This IRIDA plugin implement ECTyper version release 0.9.0 that brought the following beneficial features:

• fall back to single O-antigen signature detection (e.g.wzx )when both signature pairs are not found and when species is E.coli
• improved O-antigen identification favouring presence of both alleles (e.g. wzx and wzy) to support the final antigen call. The sum of scores for both alleles of the same antigen is used in ranking now
• verification for E.albertii species against RefSeq genomes
• addition of Quality Control flags in the output (as an extra column in the results.tsv) for ease of results interpretation
• species reporting to better resolve E.coli vs Shigella vs E.albertii cases and contamination
• serotype prediction for all Escherichia genus to ease classification of cryptic spqeices
• automatic download of the RefSeq sketch and associated meta data every 6 months for improved species identification
• improved species identification for the FASTQ files. All raw reads are used for species identification
• better complex cases handling and error recovery in cases of poor reference allele coverage giving higher specificity and sensitivity
• query length coverage default threshold lowered from 50% to 10% for truncated alleles. This greatly improved sensitivity.
• serotype reporting based on multiple evidences including reference allele database and closest reference genome
• users is warned about potential false postive result in case of non-E.coli species or assembly errors
• wrote additional unit tests

First IRIDA plugin working on the raw reads

This release uses raw paired Illumina reads to make predictions on E.coli serotype. This is release should work both on 19.05 and 18.05 Galaxy versions. Previous pre-release did not run on the development IRIDA instance but this should not be the case for this release