shigatyper

ShigaTyper

ShigaTyper is meant to work on Illumina reads, but it appears to work... fine on fasta files which is why it is included in Grandeur

About: |

ShigaTyper is a quick and easy tool designed to determine Shigella serotype using Illumina (single or paired-end) or Oxford Nanopore reads with low computation requirement.

Documentation : https://github.com/CFSAN-Biostatistics/shigatyper

Citation : https://journals.asm.org/doi/10.1128/aem.00165-19

Directory tree:

shigatyper/
├── sample_shigatyper-hits.tsv
├── sample_shigatyper.tsv
├── shigatyper_hits.txt
└── shigatyper_summary.txt

Example file for an individual sample (sample_shigatyper-hits.tsv)

sample		Hit	Number of reads
ecoli_GCA_003019175.1	0	EclacY	1
ecoli_GCA_003019175.1	1	cadA	1

Example file for an individual sample (sample_shigatyper.tsv)

sample	prediction	ipaB	notes
ecoli_GCA_003019175.1	Not Shigella or EIEC	-	ecoli_GCA_003019175.1 is ipaH-.

Example file for a run (shigatyper_hits.txt)

sample		Hit	Number of reads
ecoli_GCA_003019175.1	0	EclacY	1
ecoli_GCA_003019175.1	1	cadA	1
ecoli_GCA_009738455.1	0	EclacY	1
ecoli_GCA_009738455.1	1	cadA	1
ecoli_GCA_023823105.1	0	EclacY	1
ecoli_GCA_023823105.1	1	cadA	1

Example file for a run (shigatyper_summary.txt)

sample	prediction	ipaB	notes
ecoli_GCA_003019175.1	Not Shigella or EIEC	-	ecoli_GCA_003019175.1 is ipaH-.
ecoli_GCA_009738455.1	Not Shigella or EIEC	-	ecoli_GCA_009738455.1 is ipaH-.
ecoli_GCA_023823105.1	Not Shigella or EIEC	-	ecoli_GCA_023823105.1 is ipaH-.