Pulling together contigs: a less stringent assembly

[nwfungi]

Greetings,

New grad student here working with a fungi with a genome that is roughly 42-50Mbs. Basically what I'm trying to do is an assembly with filtered sub reads in fastq format which came from a set of PacBio sequencing. Any recommendations on programs to use to assemble these would be much appreciated.

Also interested in combining assembly data from different sequencing technologies (Ion torrent, Illumnia, and PacBio) to create an overall better assembly and again would love to have a program recommended to start looking at.

[Brian Bushnell]

I recommend Falcon, which comes from PacBio. I don't use it personally, though, I just work with people who do, so I can't give you any specific advice.

[GenoMax]

If you have access to PacBio SMRTportal (and original data files) you could do the alignment via the GUI. This would probably use the assembler @Brian referred to (I will have to look).

[rhall]

Do you have any idea about the ploidy of the sample that was sequenced? Falcon will perform better on a diploid ( or possibly multiploid ), but if the sample is haploid the HGAP pipeline in SMRT Portal should give good results. Do you have access to the primary sequencing data *.bax.h5, although you can run Falcon without it you will need it eventually to quiver correct the assembly and get the highest quality output.
As for including other data types, if you have enough coverage, likely given the small size of the genome, I wouldn't worry about using the other data until you have an assembly. At that point the other data can be mapped against the assembly to check quality.

[flxlex]

I would have a look at https://github.com/PacificBioscience...Bio-Long-Reads, which has many suggestions.