croler (please, all letters lowercased) is genome OLC de novo assembler written on FER, under leadership of Mile Sikic.

As most OLC assemblers do, croler consists of three different phases:

• overlap
• layout
• consensus

[for details follow the links above].

• gcc (4.7.2 on debian will do the job)
• make

Change the directory where the project is cloned and make sure that following commands flow through your command line

git submodule update --init --recursive
make

When build process finishes (successful, eventually), the bin directory will contain symlinks to binaries of different stages: croler_overlap, croler_layout and croler_consensus. We think that names are verbose enough to not explain it which binary refers to which stage.

croler reads input in .afg (AMOS) format

It can be run multiple ways. The simplest way is to use run.sh script like

./run.sh <reads.afg>

The example runs the all phases, pipelined, with default parameters. Resulting contigs will be saved in {reads}_consensus.fasta file. Feel free to explore other side-effect files (intermediate results), such as {reads}_overlaps.afg, {reads}_layout.afg and various .dot graphs created by layout phase.

{reads} refers to a prefix of reads filename

Note: It is the simplest way to run the assembly, but running each phase separetely is more flexible and allows adjusting parameters to your test data. We really encourage you to explore the running options of each phase.

Converting .fasta files to .afg could be done with AMOS toAmos tool with

toAmos -o output.afg -s reads.fasta

Jump to tests.

• Bruno Rahle
• Anton Grbin
• Mario Kostelac ([email protected])
• Marko Culinovic ([email protected]).

Do not hesitate to drop an email to Marko and Mario, if you have any questions.