Standard Operating Procedures
This generates the masurca template file and names it config.txt
module load masurca/3.4.2
masurca -g config.txt
# example configuration file
# DATA is specified as type {PE,JUMP,OTHER,PACBIO} and 5 fields:
# 1)two_letter_prefix 2)mean 3)stdev 4)fastq(.gz)_fwd_reads
# 5)fastq(.gz)_rev_reads. The PE reads are always assumed to be
# innies, i.e. --->.<---, and JUMP are assumed to be outties
# <---.--->. If there are any jump libraries that are innies, such as
# longjump, specify them as JUMP and specify NEGATIVE mean. Reverse reads
# are optional for PE libraries and mandatory for JUMP libraries. Any
# OTHER sequence data (454, Sanger, Ion torrent, etc) must be first
# converted into Celera Assembler compatible .frg files (see
# http://wgs-assembler.sourceforge.com)
DATA
#Illumina paired end reads supplied as <two-character prefix> <fragment mean> <fragment stdev> <forward_reads> <reverse_reads>
#if single-end, do not specify <reverse_reads>
#MUST HAVE Illumina paired end reads to use MaSuRCA
PE= pe 500 50 input/Illumina/JES_119_R1.fq.gz input/Illumina/JES_119_R2.fq.gz
#Illumina mate pair reads supplied as <two-character prefix> <fragment mean> <fragment stdev> <forward_reads> <reverse_reads>
#JUMP= sh 3600 200 /FULL_PATH/short_1.fastq /FULL_PATH/short_2.fastq
#pacbio OR nanopore reads must be in a single fasta or fastq file with absolute path, can be gzipped
#if you have both types of reads supply them both as NANOPORE type
#PACBIO=/FULL_PATH/pacbio.fa
# we may need to filter this
NANOPORE=input/Nanopore/Nanopore_JES119_20190627.fq.gz
#Legacy reads (Sanger, 454, etc) in one frg file, concatenate your frg files into one if you have many
#OTHER=/FULL_PATH/file.frg
#synteny-assisted assembly, concatenate all reference genomes into one reference.fa; works for Illumina-only data
#REFERENCE=/FULL_PATH/nanopore.fa
END
PARAMETERS
#PLEASE READ all comments to essential parameters below, and set the parameters according to your project
#set this to 1 if your Illumina jumping library reads are shorter than 100bp
EXTEND_JUMP_READS=0
#this is k-mer size for deBruijn graph values between 25 and 127 are supported, auto will compute the optimal size based on the read data and GC content
GRAPH_KMER_SIZE = auto
#set this to 1 for all Illumina-only assemblies
#set this to 0 if you have more than 15x coverage by long reads (Pacbio or Nanopore) or any other long reads/mate pairs (Illumina MP, Sanger, 454, etc)
USE_LINKING_MATES = 0
#specifies whether to run the assembly on the grid
USE_GRID=0
#specifies grid engine to use SGE or SLURM
GRID_ENGINE=SLURM
#specifies queue (for SGE) or partition (for SLURM) to use when running on the grid MANDATORY
GRID_QUEUE=batch
#batch size in the amount of long read sequence for each batch on the grid
GRID_BATCH_SIZE=500000000
#use at most this much coverage by the longest Pacbio or Nanopore reads, discard the rest of the reads
#can increase this to 30 or 35 if your reads are short (N50<7000bp)
LHE_COVERAGE=35
#set to 0 (default) to do two passes of mega-reads for slower, but higher quality assembly, otherwise set to 1
MEGA_READS_ONE_PASS=0
#this parameter is useful if you have too many Illumina jumping library mates. Typically set it to 60 for bacteria and 300 for the other organisms
LIMIT_JUMP_COVERAGE = 300
#these are the additional parameters to Celera Assembler; do not worry about performance, number or processors or batch sizes -- these are computed automatically.
#CABOG ASSEMBLY ONLY: set cgwErrorRate=0.25 for bacteria and 0.1<=cgwErrorRate<=0.15 for other organisms.
CA_PARAMETERS = cgwErrorRate=0.15
#CABOG ASSEMBLY ONLY: whether to attempt to close gaps in scaffolds with Illumina or long read data
CLOSE_GAPS=1
#number of cpus to use, set this to the number of CPUs/threads per node you will be using
NUM_THREADS = 24
#this is mandatory jellyfish hash size -- a safe value is estimated_genome_size*20
JF_SIZE = 200000000
#ILLUMINA ONLY. Set this to 1 to use SOAPdenovo contigging/scaffolding module.
#Assembly will be worse but will run faster. Useful for very large (>=8Gbp) genomes from Illumina-only data
SOAP_ASSEMBLY=0
#If you are doing Hybrid Illumina paired end + Nanopore/PacBio assembly ONLY (no Illumina mate pairs or OTHER frg files).
#Set this to 1 to use Flye assembler for final assembly of corrected mega-reads.
#A lot faster than CABOG, AND QUALITY IS THE SAME OR BETTER.
#Works well even when MEGA_READS_ONE_PASS is set to 1.
#DO NOT use if you have less than 15x coverage by long reads.
FLYE_ASSEMBLY=1
END
Now run masurca to generate the run steps
masurca config.txt # will generate assemble.sh
sbatch -p intel -n 24 -N 1 --mem 64gb assemble.sh # submit this as a job