##Lola
This repository contains the code for the program Lola which assembles Moleculo reads (now called Illumina TruSeq synthetic reads). Important note: our results show that minimus2 from the AMOS package does a better job in assembling Moleculo long reads and it is also much faster and easy to use. We therefore recommend that you use Minimus2 instead of Lola for this purpose. If you do choose to use Lola then here are some instructions.
The process of assembling long reads with Lola consists of the following two steps:
- Determining overlaps between the reads using the program overlap, and
- Running Lola
For running overlap refer to the README file for the overlap project. For running Lola use the following command:
$ <path-to-Lola-directory>/assemble.pl
You can get a description of the parameters taken by Lola by running this command without parameters:
$ ./assemble.pl
Usage: ./assemble.pl [-p <% identity threshold] <sequence-file> <connection-file1> [... <connection-filen>] <out-prefix>
Parameters are:
- % identity threshold - minimum % identity to be used by Lola for considering overlaps between reads.
- sequence file - that's the file with the reads you want to assemble
- connection-file - that's the output file from the program overlap
- out-prefix - prefix for names of files that will be generated by Lola.
Output consists of the following files:
- <out-prefix>.fna - File with both assembled contigs and unassembled reads. Assembled reads and reads contained in other reads are excluded from this file.
- <out-prefix>.gff - mapping of reads to assembled contigs and other reads (in case a read is contained within another read).
- <out-prefix>.log - a log file describing the assembly decision making process.
- <out-prefix>.progress.log - another log file with debugging information.
The directory example under this repository contains an example for how to run Lola. Modify path to Lola and overlap in the run file under this directory and then do
$ example/run
Check example/output for what the directory should look like after run finishes.
Comming soon
Copyright (C) 2014 Itai Sharon
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