PARAMETERS.md

Input/output options

Define where the pipeline should find input data and save output data.

Parameter	Description	Default
outdir	The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
gendir	The input directory that contains a genomic FASTA file ('.fna','.fasta') and a GFF3 annotation file ('.gff','.gff3') for each genome (focal and neighbors).

Required input values

Parameter	Description	Default
focal	The name of the focal genome (the one whose CDS will be tested).
strategy	The strategy number to apply to detect denovo genes : 1-> has a non-coding hit 'outgroup' (see https://github.com/Proginski/dense/tree/master#outgroup) i.e. has a non-coding hit in a genome without any CDS hit AND that genome has an older MRCA than any genome with a CDS hit ; 2-> has a non-coding hit, i.e. TRG has a non-coding hit in a genome without any CDS hit ; 3-> has no (but self) coding hit and has a non-coding hit	1

Other important parameters

Parameter	Description	Default
tree	The phylogenetic tree that shows relations between the genomes (Newick format). E.g. "((Ptep:0.75680000,Pruf:0.75680000)'210':0.38205000,Pfoa:1.13885000)'220';"
num_outgroups	The required number of outgroups with a non-coding match for the strategy 1 (see https://github.com/Proginski/dense/tree/master#outgroup)	1
elongation_size	Which size to elongate on each side of the CDS when looking for homology.	99
help	Throws this page.

Institutional config options

Parameters used to describe centralised config profiles. These should not be edited.

Parameter	Description	Default
config_profile_name	Institutional config name.
config_profile_description	Institutional config description.

Max job request options

Set the top limit for requested resources for any single job.

Parameter	Description	Default
max_cpus	Maximum number of CPUs that can be requested for any single job.	16
max_memory	Maximum amount of memory that can be requested for any single job.	128.GB
max_time	Maximum amount of time that can be requested for any single job.	240.h

TRG list options

Parameter	Description	Default
trgsblastdir	A directory with the (precomputed) BLAST output necessary for TRG homologs detection. Two files per neighbor genome, must be named 'TRG_multielongated_blastp_${neighbor}CDS_elongated.out' and 'TRG_multielongated_tblastn${neighbor}_genome.out'. Incompatible with the following parameters.
trgs	A text file with a predefined list of CDS to consider as TRGs (incompatible with the following parameters).
genera_out	A '.tsv' file with precomputed gene ages from genEra. Makes '--genera_db' useless.
genera_db	Path to the diamond db with taxonomy (e.g. '../DBs/nr.dmnd'). Necessary if a list of TRGs is not provided ('--TRGs').
genera_fast	Use a custom version of GenEra to deal with large genomes. Warning : may open as many files as the number of CDSs.	False
taxdump	The taxdump directory path (otherwise downloaded).
taxids	A '.tsv' file with two columns : col1 = genome name, col2 = taxid. Must include all genomes (focal and neighbors).
trg_node	A taxonomic node (e.g. Mammalia) to filter CDS into TRGs. CDS associated with this node or on of ots children will be considered as TRGs (incompatible with '--trg_rank').
trg_rank	A taxonomic rank (e.g. 'order') to filter CDS into TRGs. CDS associated with this node or on of ots children will be considered as TRGs (incompatible with '--trg_node').	genus

Synteny checking

Parameter	Description	Default
synteny	Whether or not the check is TRGs are in synteny with their non-coding homolog(s). Required by the following parameters.	True
synteny_window	The number of flanking genes to collect on each side (5' and 3') of the TRG and on each side of its non-coding hit.	4
synteny_anchors	The minimum number of genes on each side of the TRG that should have their ortholog on one side of its non-coding hit. E.g. : out of 4 flanking genes (set with synteny_window), 3 upstream genes have their ortholog among the flanking genes of the non-coding hit, and 2 for downtream genes. The synteny will be assumed if synteny_anchors is set to 1 or 2, but not 3 or more, because there are only 2 'anchors' on the downstream side of the query.	1
orthodir	A directory with the precomputed pairs of orthologous genes for each focal-neighbor genomes pair. One file per genomes pair, must be named '${focal}_${neighbor}_orthologs.tsv'. Incompatible with the following parameters.
orthotool	The tool to perform alignments for orthologs definition.	diamond
diamond_sens	Diamond sensitivity.