error correcting pacbio reads

[markcharder]

Hi all,

I have some pacbio fastq files from a recent experiment and some illumina fastqs, all genomic sequences.

My plan for these data is to error-correct the pacbio with the illumina.

For error correction there seem to be two protocols, one uses the command 'PBcR' whereas the other uses 'pacBio TocA'. I have wgs 8.2 but not the SMRT analysis environment. It says pacBio ToCA requires the SMRT analysis environment but for 'PBcR' it doesn't seem to be mentioned anywhere.

I was wondering what the difference is between these two commands and whether both require the SMRT analysis environment?

furthermore, I am planning to use pbjelly later on to gap-fill a Sanger sequence with the error-corrected pacbio. It says nothing in the supporting documentation but in the PBJelly publication it says it assembles the data using the ALLORA assembler from the AMOS suite, which is in the SMRT analysis environment (I believe). Can it use another assembler or does it also require installation of the SMRT analysis environment?

Would be very grateful for any advice on this, I am very new to genome assembly and any kind of command line-based computational analysis.

Mark

[flxlex]

PacBioToCa has afaik been superseded by PBcR. You can either use the smrtanalysis, or wgs-assembler (aka Celera Assembler) installation for this.

PBJelly does not seem to depend on smrtanalysis (but it needs blasr and other things). Also, you can use the raw PacBio reads for PbJelly.

[markcharder]

PacBioToCa has afaik been superseded by PBcR. You can either use the smrtanalysis, or wgs-assembler (aka Celera Assembler) installation for this.

PBJelly does not seem to depend on smrtanalysis (but it needs blasr and other things). Also, you can use the raw PacBio reads for PbJelly.

Thanks a lot for your reply, that makes sense.

Mark