Computing Resource

Mecat

We suggest 5Gb memory and 16 cpu for mecat alignment.

PBJelly

The size of memory depends on the file size of the fastq. Usually 15Gb fastq input requires 20Gb for blasr alignment. Since run_pbjelly have filtered most of reads, ~80%, we recommend 2Gb memory and 20 cpu for blasr alignment and 16 cpu for the local assembly in PBJelly.

You can easily change these settings in the config.cfg file.

Storage

For a genome ~600Mb size with 100x PacBio, the storage for each folder is:

Folder	Storage	Description
0-shells	1.8M	Store all the shells
1-data	61G	Store the filted fasta file and as input for mecat
2-results	9.9G	Store the mecat results, picked fastq file and PBJelly results
3-reports	5.5K	Store reports for run_pbjelly (just a txt file now)
4-logs	340G	Store log file for run_pbjelly and tmp file for mecat alignement(Count for the vast majority)

To save you storage, you can nohup the shell ‘nohup_rm.sh’ after you finished runpbjelly.