Hello,
I would like to know what is best for bacteria genome assembly in general. I work on 4M~6M genomes in general and they have 1 or 2 chromosomes with some plasmids. But I have more contigs than I expected them to be, so I would like to get reduced contigs.
I leave all parameters by default except genome size and I use HGAP3. So I am wondering if there are more options get reduced contigs, apart from genome size and using HGAP2. raising Target coverage or any other parameters help to get reduced contigs?
I work with PacBio20K and after running SMRT analysis (HGAP3) I usually got 80x for a chromosome but sometimes I got more than 100x for a chromosome.
Sorry about my English if it bothers you.
any advice would be appreciated.
Thanks.
I would like to know what is best for bacteria genome assembly in general. I work on 4M~6M genomes in general and they have 1 or 2 chromosomes with some plasmids. But I have more contigs than I expected them to be, so I would like to get reduced contigs.
I leave all parameters by default except genome size and I use HGAP3. So I am wondering if there are more options get reduced contigs, apart from genome size and using HGAP2. raising Target coverage or any other parameters help to get reduced contigs?
I work with PacBio20K and after running SMRT analysis (HGAP3) I usually got 80x for a chromosome but sometimes I got more than 100x for a chromosome.
Sorry about my English if it bothers you.
any advice would be appreciated.
Thanks.
Comment