Supported Tools

PIPA includes 48 bioinformatics tools organized into 7 categories.

Trimming Tools

Tool	Purpose	Reference
Trim Galore	Quality/adapter trimming for Illumina	Krueger F (2012)
Porechop_ABI	Adapter removal for Nanopore	Bonenfant Q et al. (2023)

Assembly Tools

Tool	Purpose	Reference
SPAdes	Short-read assembly	Bankevich A et al. (2012)
Flye	Long-read assembly	Kolmogorov M et al. (2019)
Unicycler	Hybrid assembly	Wick RR et al. (2017)
Canu	Long-read assembly	Koren S et al. (2017)

General Annotation

Tool	Purpose	Reference
Prokka	Gene annotation (CDS, rRNA, tRNA)	Seemann T (2014)
Bakta	Rapid bacterial genome annotation	Schwengers O et al. (2021)
MLST	Multi-locus sequence typing	Seemann T
Barrnap	Ribosomal RNA prediction	Seemann T
tRNAscan-SE	tRNA prediction	Chan PP & Lowe TM (2019)
EggNOG-mapper	Functional annotation (orthologous groups)	Cantalapiedra CP et al. (2021)
KOFAM	KEGG functional annotation	Aramaki T et al. (2020)

Assembly Quality

Tool	Purpose	Reference
BUSCO	Assembly completeness assessment	Manni M et al. (2021)
CheckM	Assembly quality assessment	Parks DH et al. (2015)
QUAST	Contig quality assessment	Gurevich A et al. (2013)

Resistance & Virulence

Tool	Purpose	Reference
Abricate	Resistance gene screening (NCBI)	Seemann T
Abricate VFDB	Virulence factor detection (VFDB)	Seemann T
AMRFinderPlus	NCBI AMR detection	Feldgarden M et al. (2021)
mcroni	Colistin resistance (mcr-1 variation)	Shaw LP et al.

Mobile Elements & Defense

Tool	Purpose	Reference
PlasmidFinder	Plasmid replicon identification	Carattoli A et al. (2014)
MOB-suite	Plasmid classification and typing	Robertson J et al. (2018)
Phigaro	Prophage region detection	Starikova EV et al. (2020)
PhiSpy	Prophage prediction	Akhter S et al. (2012)
CRISPRCasFinder	CRISPR array and Cas gene detection	Couvin D et al. (2018)
DefenseFinder	Anti-phage system detection	Tesson F et al. (2022)
ISMapper	Insertion site identification	Hawkey J et al. (2015)

Organism-Specific Typing

Tool	Organism	Purpose	Reference
Kleborate	Klebsiella	Virulence and resistance typing	Lam MMC et al. (2021)
staphtyper	Staphylococcus aureus	agr, spa, SCCmec typing	Petit RA
TBProfiler	Mycobacterium tuberculosis	Resistance and lineage detection	Phelan JE et al. (2019)
ClermonTyping	Escherichia	Phylotyping	Beghain J et al. (2018)
ECTyper	Escherichia coli	Serotype prediction	Laing C et al. (2014)
emmtyper	Streptococcus pyogenes	emm-typing	MDU-PHL
GenoTyphi	Salmonella Typhi	Genotyping	Wong VK et al. (2016)
hicap	Haemophilus influenzae	Cap locus serotype	Watts SC & Holt KE (2019)
HpSuisSero	Haemophilus parasuis	Serotype prediction	Liu J
legsta	Legionella pneumophila	Typing	Seemann T
LisSero	Listeria monocytogenes	Serogroup prediction	MDU-PHL
meningotype	Neisseria meningitidis	Serotyping	MDU-PHL
ngmaster	Neisseria gonorrhoeae	Multi-antigen ST	MDU-PHL
pasty	Pseudomonas aeruginosa	Serogrouping	Petit RA
pbptyper	Streptococcus pneumoniae	PBP typing	Petit RA
PneumoCaT	Streptococcus pneumoniae	Capsular typing	Kapatai G et al. (2016)
sccmec	Staphylococcus aureus	SCCmec typing	Petit RA
SeqSero2	Salmonella	Serotype prediction	Zhang S et al. (2019)
SeroBA	Streptococcus pneumoniae	Serotyping from reads	Epping L et al. (2018)
ShigaPass	Shigella	Serotype prediction	Yassine I et al.
ShigaTyper	Shigella	Serotype from reads	Wu Y et al. (2019)
ShigEiFinder	Shigella/EIEC	Serotyping	Lan R et al.
SISTR	Salmonella	Serovar prediction	Yoshida CE et al. (2016)
spaTyper	Staphylococcus aureus	spa typing	Sanchez-Herrero JF
SsuisSero	Streptococcus suis	Serotype prediction	Liu J
staphopia-sccmec	Staphylococcus aureus	SCCmec typing	Petit RA & Read TD (2018)
STECFinder	Escherichia coli (STEC)	Serotyping	Lan R et al.