Jason Chin

@msc51 even for large genome work done here, I have never seen the consensus running longer than one day. (We do have quite reasonable file system here.) Can you dump...

Can you try `--n_core 8` rather than `--n_core 64`?

well, I don't know how your system really work. If you want to try the different parameter, yes, you stop it and make sure all remaining running jobs are actually...

Please take a look at this https://www.dropbox.com/s/o1wid0ia6ml104i/Falcon_Internal_Sec1.pdf it is a design choice to not include the first read of the overlaps used to layout contigs as the read can appear...

``` The file ctg_paths encodes the graph for each contig after the unitigs are analyzed and put into contigs. Each line has 7 columns. The first column is the contig...

If you run it again, you might want to have a clean working directory to have a fresh start. (This may not desirable for large genome though. In such cases,...

Since you are nearby, we should meet face to face next time @pb-cdunn is in town.

Hi, @prince26121991, the general principle of FALCON design follows this publication http://www.nature.com/nmeth/journal/v10/n6/full/nmeth.2474.html You can also check https://speakerdeck.com/jchin/string-graph-assembly-for-diploid-genomes-with-long-reads and https://speakerdeck.com/jchin/de-novo-diploid-genome-assembly-and-haplotype-sequence-reconstruction (FALCON itself does not separate the haplotypes though)

@prince26121991 FALCON is not designed to handle hybrid corrected reads. While it works for some error corrected reads by setting the input type as "preads", you need to be careful....

please check http://www.nature.com/nmeth/journal/v13/n12/extref/nmeth.4035-S1.pdf Supplementary Figure 13 to 15 and associated text.