Running assisted assemblies with runAssembly

[Broadie]

Hello,

I am trying to figure out how to run an assisted assembly with runAssembly. I have been told that you can give runAssembly fasta files in addition to the sff files you want to assemble. I have a reference fasta and I tried giving this to run assembly in addition to the sff files and it skipped it:
Warning: Long read Contig3893 (27001 bp) too long to be assembled. Skipping...

Anyway to get runAssembly to assemble this? I suppose I could shred the fasta into shorter sequences into a multi fasta but that would somewhat defeat the purpose of doing an assisted assembly. Any help is appreciated.

[kmcarr]

Broadie,

runAssembly is strictly a de novo assembly tool. It is true that you can also pass FASTA files to runAssembly but this is not to provide a reference, just additional, non-454 generated read data (e.g. Sanger sequence).

To perform an assisted (mapping) assembly you need to use the program runMapping. You could also use the project based commands: newMapping, setRef, addRun, runProject, or you could use gsMapper (same underlying programs but with a GUI on top.)

[Tuxido]

The Roche mapping (or assembly) software uses a max of 2000bp for a read. So if you which to map reads that are longer than this (Contig3893) it will not run.

So you should use another mapper program for this (we did it in CLCBio)

[waterboy]

Hello,
Can any one please tell me how to use Newbler's scaffolder, I have contigs and 454 PE reads for scaffolding.

I tried scaffolding using newbler gsAssembler, but I got the following warnings

Warning: Long read single_contig1|size2654 (2654 bp) too long to be assembled. Skipping...
Warning: Long read single_contig2|size5564 (5564 bp) too long to be assembled. Skipping...
Warning: Long read single_contig4|size24776 (24776 bp) too long to be assembled. Skipping...
Warning: Long read single_contig5|size14460 (14460 bp) too long to be assembled. Skipping...
Warning: Long read single_contig6|size4969 (4969 bp) too long to be assembled. Skipping...
Warning: Long read single_contig7|size5569 (5569 bp) too long to be assembled. Skipping...
Warning: Long read single_contig8|size10954 (10954 bp) too long to be assembled. Skipping...
Warning: Long read single_contig9|size3906 (3906 bp) too long to be assembled. Skipping...
Warning: Long read single_contig10|size5173 (5173 bp) too long to be assembled. Skipping...
Warning: Input contains many reads too long to be assembled.

Please guide me on these warnings and will you please tell me how you used Newbler scaffolder.

Look forward to hearing from you.