Solexa.abi and 454 seq data.

[Jordy224]

Greetings, I am new to assembly please bear with me .

Question: Is Mira or Velvet compatible with Solexa.abi.contigs and 454 reads?

Input:
ch_abi_contigs.fa
No of Sequences = 2527
Total Sequence Length = 10686451
ch_454_reads.fa
No of Sequences = 400440
Total Sequence Length = 102044021

Results:
Velvet output:
No of Sequences = 9142
Total Sequence Length = 9162684
Mira output
None
* returns preprossing outputs with the –output parameter but no shorter contigs are observed. abi data is used as a backbone to the 454 sequence data.

-Jordy

[bioinfosm]

What do you mean by solexa.abi? Combining solexa and abi data together?
How come your input is contigs? I am not sure I understood..

[Jordy224]

Yes, and the data was assembled into contigs. The contigs have multiple gaps that I am attempting to resolve with 454 data.

For example I am using...

Mira with "ch_454_reads" to map against the "ch_abi_contig" backbone using the -SB command “strainbackbone”

as shown above velvet is chopping up the contigs!

[bioinfosm]

Ok.. maybe I am not reading it right, but what do you mean by velvet is chopping up the contigs?

Thanks