Hi
I need some advice how to cost efficiently sequence 3-4 invertebrate genomes of around 100Mb. I have some experience from a related genome where we had 2x150bp reads, an insert of 500bp and 80x coverage. I was not involved in the sequencing strategy, I simply got the sequences.
The assembly worked quite good: I got an N50 of 115kb and I could further improve the N50 to 350kb with a secondary assembly guided by a closely related published reference genome.
The guided assembly will not be possible with the other genomes and to get comparable results I would like to improve the Illumina sequencing. Naively I was thinking longer reads, longer insert and higher coverage would be better but I have some difficulties to get an overview what the different instruments are capable off, what the companies offer and what they charge. I mean Illumina PE alone because I don't think we can afford a combination with Mate-Pair or PacBio. This is what I know for now:
- We got an offer for $1,400 from a sequencing company for 2x125 (why not 150 on HiSeq 2500?), an insert of 550bp and 110x coverage. But this doesn't look more promising, right? I guess the higher coverage will just outweigh the shorter reads?
- As far as I know the only possibility for longer reads with Illumina are MiSeq platforms, but these are more expensive because of the lower output, right?
Any suggestions for an affordable (around $1,500 per 100Mb genome) Illumina only strategy ?
Thank you!
I need some advice how to cost efficiently sequence 3-4 invertebrate genomes of around 100Mb. I have some experience from a related genome where we had 2x150bp reads, an insert of 500bp and 80x coverage. I was not involved in the sequencing strategy, I simply got the sequences.
The assembly worked quite good: I got an N50 of 115kb and I could further improve the N50 to 350kb with a secondary assembly guided by a closely related published reference genome.
The guided assembly will not be possible with the other genomes and to get comparable results I would like to improve the Illumina sequencing. Naively I was thinking longer reads, longer insert and higher coverage would be better but I have some difficulties to get an overview what the different instruments are capable off, what the companies offer and what they charge. I mean Illumina PE alone because I don't think we can afford a combination with Mate-Pair or PacBio. This is what I know for now:
- We got an offer for $1,400 from a sequencing company for 2x125 (why not 150 on HiSeq 2500?), an insert of 550bp and 110x coverage. But this doesn't look more promising, right? I guess the higher coverage will just outweigh the shorter reads?
- As far as I know the only possibility for longer reads with Illumina are MiSeq platforms, but these are more expensive because of the lower output, right?
Any suggestions for an affordable (around $1,500 per 100Mb genome) Illumina only strategy ?
Thank you!
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