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A7_conf.ini
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A7_conf.ini
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###############################################################################
# Project Settings.
#
PROJECT_NAME="/home/projects/ku_00039/people/joeviz/stlfr_assembly/slrsuperscaffolder/GAGA-0580/slr_output" #name of work dirctory
THREADS=20 #num of threads
###############################################################################
# Tool settings
#
STLFR_ASSEMBLER_DIR=/home/projects/ku_00039/people/joeviz/programs/SLR-superscaffolder/SLR-superscaffolder_installed/ # stLFR Scaffold Assembler installation directory
BWA_DIR=/services/tools/bwa/0.7.16a/ # BWA installation directory
###############################################################################
# Input data settings
#
# MAKE SURE ALL PATH ARE ABSOLUTELY PATH.
# DO NOT USE "../" "~/" "./" !!!
#
## for input stLFR reads
R1="/home/projects/ku_00039/people/joeviz/data/GAGA-0580/split_reads.1.fq.gz.clean" # the read1 of stLFR reads
R2="/home/projects/ku_00039/people/joeviz/data/GAGA-0580/split_reads.2.fq.gz.clean" # the read2 of stLFR reads
## for input contig
SOAP_DIR="/home/projects/ku_00039/people/joeviz/stlfr_assembly/slrsuperscaffolder/GAGA-0580" # the input contigs directory
SOAP_K=63 # the used-k-value of SOAPdenovo. If contigs are not generated using SOAPdenovo, then keep it as 63.
PREFIX="GAGA-0580_Probolomyrmex_longiscapus_Masurca" # the prefix of you contig/ContigIndex
###############################################################################
# Control parameter settings
#
###################################################
# for step 1 bwa mem
BWA_K=53 # the mapping k-value for bwa
###################################################
# for step 2 order
MST_BIN_SIZE=7000 # the unit bin size for order.
MST_BIN_CLUSTER=0.1 # the bin cluster threshold for order.
MST_CLUSTER=0.1 # the order detect threshold.
###################################################
# for step 3 orientation
HT_BIN_SIZE=3500 # the unit bin size for orientation.
HT_BIN_CLUSTER=0.1 # the bin cluster threshold for orientation.
RANK=4 # the orientaion detect rank.
###################################################
# for step 4 pe_fill
# please make sure that SEED_MIN >= HT_BIN_SIZE * 2
MAX_INSERT_SIZE=5000 # the max allowed insert size.
PE_SEED_MIN=1000 # the min contig size to fill.
PE_SEARCH_MAX=5000 # the max search length before stop.
PE_MIN_JOINBARCODES=10 # the min joint barcode count.
PE_MIN_COUNT=3 # the min joint PE count.
PE_FILL=5 # the N size between PE-joint contigs.
###################################################
# for step 5 gap_size
GAP_BIN_SIZE=4000 # the unit bin size for gap
###################################################
# for step 6 parameters for generate sequence
#
MIN_SCONTIG=300 # the min sequence length that allows to write into the final scaffolds.
MIN_N=10 # the min N size between 2 gapped contigs.
MIN_C=1 # the min N size between 2 overlaped contigs.