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multiPrime.yaml
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multiPrime.yaml
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---
################################################################################
# directories
################################################################################
# directory, where is/are the input virus fasta file(s) located
# absolute path
input_dir: /share/data3/yangjunbo/git_storage/multiPrime/test_data
# directory, in which the pipeline writes all output files (relative to current directory)
# (this also includes the summary files)
results_dir: /share/data3/yangjunbo/git_storage/multiPrime/test_data/results
# directory to write the log-files, created during processing, to
log_dir: /share/data3/yangjunbo/git_storage/multiPrime/test_data/logs
# directory of scripts.
scripts_dir: /share/data3/yangjunbo/git_storage/multiPrime/scripts
################################################################################
# sample(s) information
################################################################################
# name(s) of the input fastq file(s)
# please type here: sample1
# this name is used throughout the entire pipeline as name for the output samples
virus:
- CDS_20727
################################################################################
# preprocessing
################################################################################
#Model selection: [fast] or [normal].
#The degeneracy of the fast model would be higher than normal. However, the advantage of the
#fast model is that it has a shorter running time compared to the normal model.
#Model: normal
#-------------------------------------------------------------------------------
# cluster by cd-hit
#-------------------------------------------------------------------------------
# identity: This parameter is linked to the "-c" option in CD-HIT, with a range of 0.65 to 1.
# We recommend setting it as 0.7 or 0.8.
# If there is a considerable similarity among the sequences in your input file,
# you may consider increasing this parameter to 0.9.
# However, it's important to note that setting it to 1 will generate primers for each individual sequence.
identity: 0.7
# seq_number_ANI: The minimum sequence number in a cluster.
# multiPrime aims to merge clusters with a size smaller than {seq_number_ANI} into larger clusters.
# This parameter helps in reducing the total number of clusters.
# If seq_number_ANI is set to 0, all clusters will be processed.
# Conversely, if seq_number_ANI is set to 1, no clusters will undergo processing.
seq_number_ANI: 1
# ani: This parameter corresponds to the whole-genome Average Nucleotide Identity (ANI).
# It defines the threshold for merging clusters,
# where only clusters with an ANI value greater than {ani} will be merged.
# The minimum value for the ANI threshold is 0.7.
ani: 0.8
# drop: This parameter determines whether to merge or drop clusters with rare sequences
# that exhibit high ANI with other clusters. If set to "T," the clusters will be dropped.
# If set to "F," the clusters will be merged into others.
drop: "F"
# max_seq: This parameter specifies the maximum number of sequences to be used
# from each cluster for multi-alignment using tools such as MUSCLE or MAFFT.
# In this step, {maxseq} sequences are randomly selected from each cluster.
# It is important to note that this selection does not impact the
# calculation of primer coverage in the final primer set.
# The coverage calculation considers all sequences within the cluster to ensure accurate results.
max_seq: 500
#-------------------------------------------------------------------------------
## primer design by multiPrime
##-------------------------------------------------------------------------------
# dege_number: This parameter, represented as "-n {}" in multiPrime-core,
# specifies the maximum number of degenerate nucleotides allowed in a primer.
dege_number: 4
# degeneracy: This parameter, represented as "-d {}" in multiPrime-core,
# denotes the maximum degeneracy allowed in a primer.
degeneracy: 10
# primer_len: This parameter, represented as "-l {}" in multiPrime-core,
# determines the length of the degenerate primers.
primer_len: 18
# variation: This parameter, represented as "-v {}" in multiPrime-core,
# indicates the maximum number of mismatches allowed during the calculation of mis-coverage.
variation: 1
# nproc: This parameter, represented as "-p {}" in multiPrime-core,
# defines the number of processes to be launched.
nproc: 1
# entropy: This parameter, represented as "-e {}" in multiPrime-core,
# measures the level of disorder or variability.
# It is used to evaluate whether a window is conserved.
# Any primer-length window with an entropy less than
# the specified value of {entropy} will be processed. The default value is 3.6.
entropy: 3.6
# coordinate: This parameter, represented as "-c {}" in multiPrime-core,
# ensures that mismatch positions are not allowed at specific sites
# within a primer during the calculation of mis-coverage.
coordinate: 2,3,-1
#-------------------------------------------------------------------------------
## get candidate primers from multiPrime output
##-------------------------------------------------------------------------------
# coverage: This parameter filters primers based on their match rate,
# which is calculated as the number of sequences that match the selected primer
# divided by the number of sequences that span the selected primer.
# Only primers with a match rate greater than the specified fraction (default: 0.6) will be retained.
# However, if the sequence number in some clusters is less than 10,
# the default coverage threshold may not be suitable.
# In such cases, you can reset the threshold.
# Additionally, if the sequence number in some clusters is very large (greater than 100,000),
# only a random subset of 500 sequences will be used to generate the output.
coverage: 0.7
# PRODUCT_size: This parameter filters primers based on the desired PCR product size.
# Primers with a product size outside the specified range (default: [250, 700]) will be filtered out.
PRODUCT_size: 150,1200
# gc_content: This parameter filters primers based on their GC content.
# Primers with a GC content outside the specified range (default: [0.45, 0.65]) will be filtered out.
gc_content: 0.2,0.7
# distance: This parameter is a filter for hairpin structures and
# represents the minimum distance between the paired bases.
# The default value is 4, and it is used to detect hairpin structures in the primer sequence.
# For example, (number of X) AGCT[XXXX]AGCT.
distance: 4
# end: This parameter filters primers based on the presence of degenerate bases at the end.
# For example, setting it to "-t 4" means that degenerate bases should not appear at the last four positions
# during the primer pre-filtering step. The default value is 4.
end: 4
# adaptor: This parameter represents the adaptor sequence used for NGS (Next-Generation Sequencing) purposes.
# It is used for hairpin or dimer detection between the adaptor and primer.
# Multiple adaptor sequences can be specified, separated by commas.
# If the adaptor sequence is unknown but an adaptor is needed for subsequent sequencing,
# the provided example sequence can be used. If no adaptor is needed, the parameter should be set as ",".
adaptor: "TCTTTCCCTACACGACGCTCTTCCGATCT,TGGAGTTCAGACGTGTGCTCTTCCGATCT"
###-------------------------------------------------------------------------------
#### get core primer set
###-------------------------------------------------------------------------------
# core_number: This parameter specifies the minimum number of sequences required in each cluster.
core_number: 10
#-------------------------------------------------------------------------------
## get max primer set from get_multiPrime
##-------------------------------------------------------------------------------
#params of get_Maxprimerset_V4.
#This step will not consider the dimer formation of 5' (primers), cause it is designed for the NGS.
#It wont form dimers between adaptors of NGS and primers.
#distance between primers; column number of primer1_F to primer2_F. Do not change this param.
#GTGTGCTCGTGACCTTGA CCACAATTGCCACGTTAG 159 3 1.0 GTGTGCTCGTGACCTTGA GGTGTCTTGTTGGAAGGG 181 3
# primer1_F Primer1_R Product_len number_match coverage primer2_F primer2_R Product_len number_match
# 1 2 3 4 5 next(1) 2 3 4
# step: This parameter represents the distance between primers and should not be changed.
step: 5
# method: This parameter determines the method used for primer selection.
# If set to "T" (true), the greedy method will be used for maximal primer selection.
# If set to "F" (false), the maximum method will be used for primer selection.
method: T