Transcript guided genome assembler.
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bin
GeneAssemblyPipeline.sh
README.md
orderContigs.py
order_and_stuff.sh
sort_fastq.sh
tasks.py

README.md

Cantina

Cantina is a transcript guided assembly pipeline. Instead of writing fresh assembly software, we exploit current assembly tools to perform local assembly around target transcripts. This allows for the assembler to focus on what is "important" and to ignore repetitive regions. Unfortunately, this will leave out things like pseudogenes and important regulatory regions of the genome which are not transcribed.

Requirements

Invoke python library, it also has some expectations about run directories so I'd take a look at tasks.py to make sure everything is configured. FastqIndex python library. You can get this here:

git@github.com:hillst/FastqIndex.git

Also expectes velvet (version not listed yet), and the ncbi-blastn

Running

to run, simply type: inv -l to get a list of command The pipeline should go as follows: sort reads/create blastdb of reads blast contigs to reads extract reads from blast hits assemble reads order reads repeat (not done yet)