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TAPIR MLST Pipeline version 1.0dev
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Mandatory arguments:
--assemblies Assembly file(s) you wish to supply as input (e.g., "/MIGE/01_DATA/03_ASSEMBLY/T055-8-G230101_FLYE/*.fasta")
--output_dir Output directory to place final combined MLST output (e.g., "/MIGE/01_DATA/03_ASSEMBLY")
--sequencing_date Sequencing Date (for TAPIR, must start with G e.g., "G230223")
Optional arguments:
--scheme For forcing a specific mlst scheme (Default: False). If true, simply supply --scheme as part of the arguments
--mlst_species Used only if the optional argument --scheme is used to force a particular mlst scheme. This must be one of
abaumannii
ranatipestifer
mcatarrhalis
aphagocytophilum
afumigatus
slugdunensis
mmassiliense
cbotulinum
bordetella
efaecium
mhyopneumoniae
otsutsugamushi
mhaemolytica
senterica
bbacilliformis
plarvae
koxytoca
chlamydiales
streptomyces
msynoviae
cglabrata
sepidermidis
pmultocida_rirdc
bcereus
soralis
sgallolyticus
kkingae
efaecalis
hparasuis
csepticum
mabscessus
tvaginalis
shominis
orhinotracheale
yruckeri
bhampsonii
shaemolyticus
sinorhizobium
saureus
bpilosicoli
sthermophilus
leptospira_2
kseptempunctata
xfastidiosa
sbsec
ctropicalis
kaerogenes
lmonocytogenes
vibrio
clari
ssuis
miowae
csinensis
ecoli
leptospira_3
ecoli_2
bhenselae
cfetus
cfreundii
spneumoniae
mhyorhinis
legionella_sbt
leptospira
hinfluenzae
chyointestinalis
magalactiae
calbicans
bintermedia
cdiphtheriae
smaltophilia
szooepidemicus
bcc
campylobacter
cupsaliensis
bhyodysenteriae
hpylori
cconcisus
sagalactiae
pgingivalis
bpseudomallei
chelveticus
tenacibaculum
scanis
csputorum
mplutonius
pacnes
hsuis
kpneumoniae
pdamselae
brachyspira
yersinia
wolbachia
cinsulaenigrae
mpneumoniae
arcobacter
vtapetis
taylorella
vvulnificus
sdysgalactiae
abaumannii_2
blicheniformis
sthermophilus_2
edwardsiella
mcaseolyticus
fpsychrophilum
dnodosus
mcanis
cdifficile
mbovis
pmultocida_multihost
brucella
spyogenes
paeruginosa
spseudintermedius
cmaltaromaticum
vparahaemolyticus
ppentosaceus
lsalivarius
vcholerae
cronobacter
pfluorescens
aeromonas
ecloacae
ckrusei
neisseria
achromobacter
borrelia
abaumannii
ypseudotuberculosis
bsubtilis
hcinaedi
suberis
clanienae
Helpful arguments:
--help This usage statement.
--version Version statement
This pipeline predicts MLST from assemblies derived from pure cultures or metagenomic samples. This Nextflow pipeline uses Torsten Tsemann's MLST tool. Module adapted from nf-core MLST module.
Inputs are fasta files specified using --assemblies.
An example of a command to run this pipeline is:
nextflow run main.nf --assemblies "assembly/Sample_file.fasta" --output_dir "test_out" --sequencing_date "G230202"
An example of a command to specify ('force') an Escherichia coli scheme is:
nextflow run main.nf --assemblies "assembly/Sample_file.fasta" --output_dir "test_out" --sequencing_date "G230202" --scheme --mlst_species ecoli
This is an ongoing project at the Microbial Genome Analysis Group, Institute for Infection Prevention and Hospital Epidemiology, Üniversitätsklinikum, Freiburg. The project is funded by BMBF, Germany, and is led by Dr. Sandra Reuter.
The TAPIR (Track Acquisition of Pathogens In Real-time) team.