Jelly − genome assembly upgrading tool
PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles. PBJelly fills or reduces as many captured gaps as possible to produce upgraded draft genomes.
For a complete description, see the help menu
−h, −−help
Show summary of options.
/usr/share/doc/pbjelly/JellyReadme.txt