Returns a parameter list with default parameter values.
parameters( wd = ".", txid = character(), mkblstdb = "", blstn = "", v = FALSE, ncps = 1, mxnds = 1e+05, mdlthrs = 3000, mnsql = 250, mxsql = 2000, mxrtry = 100, mxsqs = 50000, mxevl = 1e-10, mncvrg = 51, btchsz = 100, db_only = FALSE, outsider = FALSE, srch_trm = paste0("NOT predicted[TI] ", "NOT \"whole genome shotgun\"[TI] ", "NOT unverified[TI] ", "NOT \"synthetic construct\"[Organism] ", "NOT refseq[filter] NOT TSA[Keyword]"), date = Sys.Date() )
The working directory where all output files are saved.
Taxonomic group of interest, allows vectors.
File path to makeblastdb
File path to blastn
Print progress statements to console? Statements will always be printed to log.txt.
The number of threads to use in the local-alignment search tool.
The maximum number of nodes descending from a taxonomic group. If there are more than this number, nodes at the lower taxonomic level are analysed.
'Model organism threshold'. Taxa with more sequences than this number will be considered model organisms and a random mdlthrs subset of their sequences will be downloaded.
The minimum length of sequence in nucleotide base pairs to download.
The maximum length of sequence in nucleotide base pairs to download. Any longer sequences will be ignored.
The maximum number of attempts to make when downloading.
The maximum number of sequences to BLAST in all-vs-all searches. If there are more sequences for a node, BLAST is performed at the lower taxonomic level.
The maximum E-value for a successful BLAST.
The maximum percentile coverage defining an overlapping BLAST hit. Sequences with BLAST matches with lower values are not considered orthologous.
Batch size when querying NCBI
Take sequences only from
restezlibrary? TRUE/FALSE. If TRUE, internet is still required (for taxonomic look-up) and a
restezwill need to be set up.
om..blast? TRUE/FALSE. If TRUE, a module for running
blastnwill be installed and all BLAST commands will be run through it.
outsiderpackage is required.
Sequence NCBI search term modifier. Use this parameter to change the default search term options. Default: avoid predicted, WGS, unverified, synthetic, RefSeq and Transcriptome Shotgun Assembly sequences.
Date when pipeline was initiated