Banana Slug Genomics

# This file contains all the commands and explanations for the commands
# used to run our SOAPdenovo2 assembly of the banana slug

# Apr 28 2015
# run sparse pregraph for DBG assembly using config_file for 3 libraries
# SW018_S1_L001, SW018_S1_L007, SW019_S2_L008

SOAPdenovo2-63mer sparse_pregraph -s ../config_file -K 61 -g 15 -z 3000000000 -d 1 -e 1 -r 0 -p 20 -o soapdenovo2_sparseGraph

# -s is the configuration file
# -K is the kmer size
# -g is the max kmer edge length, number of skipped intermediate kmers
# -z is the estimated genome size
# -d is the kmer frequency cutoff, kmers with freq no larger are deleted
# -e is the kmer edge ferquency cutoff, delete kmers' related edge smaller
# -r is to kead the available read
# -p is number of cpus for use
# -o is prefix of output graph
#
# 1st Run took about 9 hours and 28 minutes on 20 cores with 50 gb memory.
# Used a total of 136080.099 CPU seconds (~37.8 CPU hours) and 59.986 Gb of max virtual memory.

SOAPdenovo2-63mer contig -p 20 -g soapdenovo2_sparseGraph

# -p is number of cpus for use
# -g is prefix of output graph from sparse_pregraph output
#
# 1st Run took about 21 minutes on 20 cores with 50 gb memory.
# Used a total of 799.740 CPU seconds (~13 CPU minutes) and 5.780 Gb of
# max virtual memory.

SOAPdenovo2-63mer map -p 20 -k 61 -s ../config_file -g soapdenovo2_sparseGraph

# -p is number of cpus for use
# -k kmer size used for mapping read to contig
# -s is the configuration file
# -g is the prefix of output graph from sparse_pregraph output
#
# 1st Run took about 2 hours and 6 minutes on 20 cores with 50 gb memory.
# Used a total of 78902.546 CPU seconds (~21.9 CPU hours) and 66.103 Gb of
# max virtual memory.

SOAPdenovo2-63mer scaff -F -p 20 -g soapdenovo2_sparseGraph

# -F fill gaps in scaffold
# -p is number of cpus for use
# -g is prefix of output graph from sparse_pregraph output
#
# 1st Run took about 24 hours and 50 minutes running on 20 cores with 50 gb
# memory.
# Used a total of 333894.594 CPU seconds (~92.7 CPU hours) and 20.366 Gb of
# max virtual memory.