Introduction

This currently hosts two projects created and maintained by Adam English.

PBJelly - the genome 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.

PBHoney - the structural variation discovery tool. PBHoney is an implementation of two variant-identification approaches designed to exploit the high mappability of long reads (i.e., greater than 10,000 bp). PBHoney considers both intra-read discordance and soft-clipped tails of long reads to identify structural variants.

For more information, visit the PBSuite web page.

Programming language: Python

Brief description: The genome upgrading tool and the structural variation discovery tool.

Open source license: custom open source license