Dear all,

I have one illumina TruSeq long read assembly and three MiSeq 2x75 short reads assemblies. I want to merge the long read assembly to each of the short reads assemblies so that at the end I will have three total assmblies:

1) Long read scaffold + Velvet scaffolds

2) Long read scaffold + AbySS scaffolds

3) Long read scaffold + SOAP scaffolds

However, I do not know how to denife the parameters in the config file, it looks like this:

[global]

mateAn_A=???

mateAn_B=???

bowtie2_read1=TSSLR-BDA11_LongRead.fastq

bowtie2_read2=oenopla-reads1.fastq

bowtie2_maxins=???

bowtie2_minins=???

bowtie2_threads=1

meta2fasta_keepUnaligned=0

meta2fasta_sizeUnaligned=??? ???

nucmer_l=50

nucmer_c=300

nucmer=/home/ktsang/.conda/envs/MyVirtualEnv/bin/nucmer

delta-filter=/home/ktsang/.conda/envs/MyVirtualEnv/bin/delta-filter

show-coords=/home/ktsang/.conda/envs/MyVirtualEnv/bin/show-coords

bowtie2=/home/ktsang/.conda/envs/MyVirtualEnv/bin/bowtie2

bowtie2-build=/home/ktsang/.conda/envs/MyVirtualEnv/bin/bowtie2-build

samtools=/home/ktsang/.conda/envs/MyVirtualEnv/bin/samtools

[1]

fasta=oenopla_VOscaffolds011216.fasta

ID=LongRead

[2]

fasta=scaffolds/SOAPdenovo.final.scaffolds.fasta

ID=SOAP

I have read the manual but I still do not understand. What number I should put at mateAn_A, mateAn_B, bowtie2_maxins, bowtie2_minins, meta2fasta?

I do not know the insert size of the short reads, can someone help/advise me with deciding he numbers in bold?

Thank you!

Kenny