v1.3.5

Release incorporating helpful changes made by @kapsakcj

v1.3.4

Added:

• an option to specify temporary directory (--tmpdir )
• a flag to not print the output header (--noheader)

v1.3.3 add single end illumina support

add single end illumina support with --single_end flag

v1.3.2

fixes:

• ungzipped input fastq file no longer causes error

changes:

• set default O antigen (wz gene) depth cutoff to 1

v1.3.1

Update to address issues identified in Yassine et al 2022

Changes

1. Adjusted SF serotype O antigen genes: only use wzx gene for SF serotyping
2. Modified the combination of SF modification genes
3. Renamed types to SB21/22,SD18 from provisional
4. Added the depth ratio variables in read mapping (reduced default for wz genes to 1):
   1. "depth” for Cluster-specific genes and virulence genes, default = 10
   2. “ipaH_depth” for ipaH gene, default = 1
   3. “O_depth” for O antigen genes, default = 1

Table 1: The depth ratio used in ShigEiFinder (read depth relative % to housekeeping genes)

Depth ratio	ShigEiFinder v1.2	ShigEiFinder v1.3
Cluster and virulence genes	10	10
ipH gene	1	1
O antigen genes	10	1

The isolates used for validation of 1.3.0

The Shigella isolates used in Yassine et al (1) (reference 316 isolates, routine 3861 isolates) were downloaded. Of these isolates, 265 reference isolates and 3840 routine isolates passed quality filters and were used for further validation.

Table 2: The accuracy of ShigEiFinder for serotyping in Yassine et al data (Ref N=265, Routine N=3840)

version	Ref - Raw reads	Ref - Genomes	Routine - Raw reads	Routine - Genomes
ShigEiFinder v1.2	82.64	84.91	55.78	84.14
ShigEiFinder v1.3	86.42	87.17	92.16	94.87

Add contamination and required files checks

When an isolate is ipaH+ but missing some or all of cluster gene set check for existense of missing genes between 1 and 10 fold coverage.
Note is added to show that original "Unclustered" assignment may be due to:

1. low coverage of one or more cluster specific genes in a real Shigella/EIEC isolate
2. Presence of a low level contaminating Shigella/EIEC in an otherwise non-Shigella/EIEC isolate

Shigeifinder packaged using setuptools

Repo structure changed to allow installation with "python setup.py install"

First full release

First full release of shigeifinder - to be used for bioconda

Initial github release

Initial Shigeifinder release, pre-publication, pre-release. Install options and pipeline not final.