Parameters¶
All parameters should be specified in the pipeline.ini configuration file
The template file can be found in ERvsearch/templates/pipeline.ini.
Make a copy of this file in your working directory (the directory where you want to run the program and store the output) and change the values of the parameters according to your system and your needs.
Required parameters¶
These parameters should always be set (there are no default options).
paths
2.1 path_to_usearch
2.2 path_to_exonerate
Optional Parameters¶
The following parameters are optional (as they have default values)
genomesplits
1.1 split
1.2 split_n
1.3 forceoutput
2.1 outfile_stemdatabase
3.1 use_custom_db
3.2 gag
3.3 pol
3.4 envusearch
5.1 min_id
5.2 min_hit_length
5.3 min_coverageplots
6.1 dpi
6.2 format
6.3 gag_colour
6.4 pol_colour
6.5 env_colourORFs
7.1 min_orf_len
7.2 translation_tabletrees
8.1 use_gene_colour
8.2 maincolour
8.3 highlightcolour
8.4 outgroupcolour
8.5 dpi
8.6 format
genomesplits¶
Parameters for dividing the input genome into batches
If the genome has more than ~100 contigs or scaffolds, it is recommended to batch these rather than running Exonerate on each contig individually, to avoid creating an excessive number of output files
The default is to split the input into 50 batches, this is a manageable number for most systems.
split¶
string True or False
Default: True
If split is True the contigs will be batched, if it is False Exonerate will run once for every gene-contig combination (usually 3x number of contigs). If there are less contigs than batches this will be ignored
force¶
string True or False
Default: False
The pipeline will error if running using these genome split settings will run Exonerate more than 500 times. If you want to force the pipeline to run despite this, change force to True.
output¶
Output file parameters
outfile_stem¶
string
Default: ERVsearch
Log files will have this as a prefix (e.g. ERVsearch_log.txt)
database¶
Parameters concerning the database of reference ERV sequences
string True or False
use_custom_db¶
Default: False
When screening using Exonerate, query sequences are used to identify ERV like regions of the genome. It is possible to use the default ERV database provided with the pipeline (recommended) or to use a custom database.
False - use the default database
True - use a custom database
gag¶
string
Default: None
Path to a custom fasta file of gag amino acid sequences. To skip this gene use None as this value (only if use_custom_db is True)
pol¶
string
Default: None
Path to a custom fasta file of pol amino acid sequences. To skip this gene use None as this value (only if use_custom_db is True).
env¶
string
Default: None
Path to a custom fasta file of env amino acid sequences. To skip this gene use None as this value (only if use_custom_db is True).
exonerate¶
Exonerate parameters
min_hit_length¶
integer
Default: 100
Minimum Exonerate hit length on the chromosome. Shorter hits are filtered out.
overlap¶
integer
Default: 30
Maximum distance between chromosome regions identified with Exonerate which are merged into single regions.
min_score¶
integer
Default: 100
Minimum score in the second exonerate pass (with ungapped algorithm).
usearch¶
USEARCH parameters
min_id¶
float
Default: 0.5
Percentage identity used by the UBLAST algorithm. Used to set the -id UBLAST parameter
min_hit_length¶
integer
Default: 100
Minimum hit length for UBLAST. Used to set the -mincols UBLAST parameter
min_coverage¶
float
Default: 0.5
Minimum proportion of the query sequence which should be covered using UBLAST. Used to set the -query_cov UBLAST parameter
plots¶
Plotting parameters
gag_colour¶
string (hex colour code with #)
Default: #f38918
Colour for gag gene in summary plots. Default is orange.
pol_colour¶
string (hex colour code with #)
Default: #4876f9
Colour for pol gene in summary plots. Default is blue.
env_colour¶
string (hex colour code with #)
Default: #d61f54
Colour for env gene in summary plots. Default is pink
other_colour¶
string (hex colour code with #)
Default: #33b54d
Colour for anything which doesn’t relate to a specific gene in summary plots. Default is green.
match_axes¶
string True or False
Default: False
If True, when gag, pol and env are shown as subplots on the same figure they should all have the same axis limits. If they do some can be very small but they are more comparable.
ORFs¶
Parameters for ORF identification
translation_table¶
integer
Default 1
Translation table to use when identifying ORFs - listed here https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi. Usually table 1 is fine - default plus alternative initiation codons
trees¶
Phylogenetic tree parameters
use_gene_colour¶
string True or False
Default: True
Use the colours specified in the plots section for each gene to highlight newly identified ERVs. If this is True, highlightcolour will be ignored and the gene colours will be used instead.If it is False, highlightcolour is used to highlight newly identified ERVs.
maincolour¶
string (hex colour code with #)
Default: #000000
Main colour for text in tree images. Default is black.
highlightcolour¶
string (hex colour code with #)
Default : #382bfe
Text colour for leaves highlighted in tree images - newly identified ERV-like regions. This is ignored if use_gene_colour above is True. Default is blue.
outgroupcolour¶
string (hex colour code with #)
Default: #0e954b
Text colour for outgroup in tree images. Default is green.
dpi¶
integer
Default: 300
Dots per inch for phylogenetic tree images.
format¶
string png, svg, pdf or jpg
Default: png
File format for phylogenetic tree images, can be svg, png, pdf or jpg
regions¶
Parameters for defining regions with ORFs from more than one retroviral gene