LSC cfg file

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    • .cfg file format

    In order to run LSC. Now, simply edit the run.cfg file and type

    runLSC run.cfg

    and that's it! An example run.cfg file is included with every LSC download and decriptions of each field can be found in the comments within the file. Detailed descriptions of each field is also below.

    .cfg syntax

    There are only three types of syntax in a .cfg file.
    Comment
    Any line begining with # is a comment. # must be the first character on the line.
    Single Value
    A single value written in the following format
    tag = value
    For example,
    genome_dir = ../../genome/hg18
    Multiple Values
    Multiple values are grouped by > and < in the following format
    > tag
    value_1
    value_2
    ...
    <

    Example .cfg file

    The following is an example .cfg file. It is included in every LSC download or you can download it here run.cfg (right-click and save as...). The values which are optional are noted in the comments and you may comment them out. 

    ##
###################################################
#
# This cofiguration file contains all settings for a run
# of LScorr.
#
# lines begining with '#' are comments
# lists begin with '> tag' and end with '<' on separate lines
#
###################################################
##

#########################
## Required Settings
##

##
# Long reads file
# (single value)

LR_pathfilename = data/LR.fa

##
# Short reads file
# (single value)

SR_pathfilename = data/SR.fa

##
# Is this nonredundant SR data set? (Y or N)
# If you have run LSC on the same SR data before, you could find it in temp folder. Its name is "SR_uniq.fa".
# You can use this "SR_uniq.fa" as the short reads file and set this option to "Y"
# (single value)

I_nonredundant = N

##
# Number of threading for short reads alignment to long reads
# (single value)

Nthread1 = 12 

##
# Number of threading for corrections
# (single value)

Nthread2 = 12

#########################

##
# Temp folder
# (single value)

temp_foldername = temp

##
# Output folder
# (single value)

output_foldername = output

##
# Length of pseudo chromosomes 
# (single value)

Lpseudochr = 50000000

##
# Length of gap sequence between long reads
# (single value)

LgapInpseudochr = 100

##
# Remove PacBio tails sub reads? (Y or N)
# The names of PacBio long reads must be in the format of the following example: ">m111006_202713_42141_c100202382555500000315044810141104_s1_p0/16/3441_3479"
# The last two numbers (3441 and 3479 in this example) are the positions of the sub reads. 
# (single value)

I_RemoveBothTails = Y

##
# Min. number of non'N' after compressing 
# (single value)

MinNumberofNonN = 39

##
# Max 'N' are allowed after compressing
# (single value)

MaxN = 1

#########################

##
# Aligner could be set to novoalign or bwa
# If you want to use BWA, you set it "aligner = bwa"

aligner = novoalign

# Aligner command options 
# Note: Do not specify number of threads, it is set through Nthread1

novoalign_options =  -r All -F FA  -n 300 -o sam -o FullNW 

bwa_options =  -n 0.08 -o 10 -e 3 -d 0 -i 0 -M 1 -O 1 -E  1 -N