I want to use a paired end library for scaffolding my contigs. I used the following command to estimate insert size using bbmap:
bbmap.sh ref=reference.fasta in1=read1.fq in2=read2.fq ihist=ihist_mapping.txt out=mapped.sam
Standard deviation is larger than mean. How would this help in scaffolding with a program like SSPACE_Standard, which uses insert size to scaffold contigs??
I have also tried estimating insert size using the script estimate_insert_size.pl that comes with SSPACE. It does not use a reference genome. Instead, it figures out the insert size by mapping paired reads on contigs. It mapped 10000 reads and gave an estimate of just the median insert size as 328. There is no information about mean and std deviation.