Command Guides

The assembler is being built as a series of modules that effect a pipeline for assembly.  The reference guides for the current modules are listed below.  Click on the name to go to the man-page for the module.

DEXTRACTOR: Tools for extracting and compressing SMRT cell data.

DAZZ_DB: Tools for building and managing a database of all the reads for a given project.

DALIGNER: Tools for computing (all) pairwise local alignments between reads and/or reference sequences.

DAMAPPER: Tools for mapping reads to reference sequences.

DAMASKER: Tools for detecting and producing masks for tandem and interspersed repetitive elements in a shotgun data set.

DASCRUBBER: Pile-based analysis tools for assessing the quality of reads, trimming low quality end, and removing all artifacts (unremoved adaptemers, chimers, low quality regions and gaps).  A partial release at this time.

DAVIEWER: A Qt-viewer for looking at and exploring read piles and mapping results.