PhytoPipe: a phytosanitary pipeline for plant pathogen detection and diagnosis using RNA-seq data

BMC Bioinformatics

Table 4 Unique features of PhytoPipe in comparison with other pipelines

	PhytoPipe	Kodoja	Pathoscope	Virtool	VirFind	VSD toolkit	VirusDetect
Platform	Local Linux	Local Linux	Local Linux	Local Linux web GUI	Web	Web	Web/Local Linux
Workflow management	Snakemake	None	None	None	None	Yabi	None
Sequencing technique	RNA seq	RNA seq	RNA seq	RNA seq	RNA seq	small RNA seq	small RNA seq
Detection of known viruses	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Novel virus discovery	Blastx + Kaiju	No	No	HMMER	Blastx	Blastx	Blastx
Detection of phytoplasma	Yes	No	Yes	No	No	No	No
Detection of bacteria	Yes	No	Yes	No	No	No	No
Detection of fungi	Yes	No	Yes	No	No	No	No
Read quality control	Yes	Yes	No	Yes	Yes	Yes	Yes
Host removal	k-mer based extraction	No	No	Host genome mapping	Host genome mapping	Host genome mapping	Host genome mapping
Ribosomal RNAs removal	Yes	No	No	No	No	No	No
Duplicates removal	Yes	No	No	No	No	No	No
Read classification	Yes	Yes	No	No	No	No	No
de novo assembly	Yes	No	No	Yes	Yes	Yes	Yes
Viral reference mapping	Yes	No	Yes	Yes	No	Yes	No
Sequence profile	Yes	No	No	No	No	No	No
Multiple samples	Yes	No	No	No	No	No	Yes

ISSN: 1471-2105