--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/default-masurca-config	Mon Jan 24 00:00:38 2022 +0000
@@ -0,0 +1,63 @@
+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  /FULL_PATH/frag_1.fastq  /FULL_PATH/frag_2.fastq
+PE= pe MEAN STDDEV INPUTREAD1 INPUTREAD2
+#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
+#PACBIO=INPUTREADLONG
+#NANOPORE=/FULL_PATH/nanopore.fa
+#NANOPORE=INPUTREADLONG
+#Other reads (Sanger, 454, etc) 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=REF
+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=defq
+#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=25
+#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 = GALAXY_SLOTS
+#this is mandatory jellyfish hash size -- a safe value is estimated_genome_size*20
+JF_SIZE = JELLYFISHSIZE
+#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=0
+END