The Gordian Assembler is a read cloud assembler for large low-copy repeat families within mammalian genomes.
This repository and setup material is currently under construction. It will soon be updated with easy to use instructions.
The Gordian Assembler depends on the phaser library, which must first be installed.
The following prerequisites must also be installed:
- idba_ud -- please use this version, which is modified both to handle longer short-read lengths and to locally assemble subsampled barcoded reads clouds. Ensure all compiled binaries are in your
$PATH
The gordian command may be run multiple times to resume the pipeline.
If an error arises, the output from gordian or the log files may
be informative.
ShortSequence: Sequence is too long. If you get this error during assembly, please make sure you are using the right fork of idba_ud.
Please submit issues on the github page for Gordian.