using bfast for mapping bacterial and viral genomes

[kakar_nipun]

Hi All

I was intending to map SOLID reads to the viral and bacterial genomes, and was thinking if i can use the same indices as mentioned in the Bfast manual, or do i need to create new ones?

After reading under advanced topics in the manual, i felt that using the same indices might just be stringent. Can someone throw some more light on this?

[nilshomer]

Hi All

I was intending to map SOLID reads to the viral and bacterial genomes, and was thinking if i can use the same indices as mentioned in the Bfast manual, or do i need to create new ones?

After reading under advanced topics in the manual, i felt that using the same indices might just be stringent. Can someone throw some more light on this?

They should work well for the viral and bacterial genomes.

[drio]

Hi All

I was intending to map SOLID reads to the viral and bacterial genomes, and was thinking if i can use the same indices as mentioned in the Bfast manual, or do i need to create new ones?

After reading under advanced topics in the manual, i felt that using the same indices might just be stringent. Can someone throw some more light on this?

There has been a lot of work behind the default indexes used for human (check support material from the paper). There is also code butil/btestindexes that
can help you test how they behave with different error rates, indels, etc... I would strongly suggest to create your own indexes (and compare with the default ones).