Requirements

• Reasonable new gcc
• Boost libraries
• Velvet
• Bowtie2
• Blasr (for Pacbio reads)

Parameters for Velvet

In our experiments we used only -cov_cutoff setting. Either set it to auto or something reasonably small. We recommend you to do the same.

Compiling GAML

cmake .
make

Running GAML

./gaml <config file>

Config file outline (check example.cfg):

Global configuration

[readset1]
readset1 configuration

[readset2]
readset2 configuration

...

Global configuration

• graph=pathtograph Required. Run Velvet on your reads and set this to LastGraph in your Velvet output directory.
• threshold=number Threshold for the length of long contigs. Default 500.
• output_prefix=filename Optional. Prefix for the output files. Defaults to "output".
• starting_assembly=filename Optional. Fasta file with starting assembly.
• max_iterations=number Optional. Maximum number of iterations for simulated annealing. Defaults to 50000.
• t0=number Optional. Initial temperature. Defaults to 0.008.
• do_proprocess=whatever If set, we do only postprocessing.
• blasr_path=path Optional. Path to BLASR (used with pacbio reads). Default "blasr/alignment/bin".

Moves configuration

All of these settings should be integers. We pick a move by selecting a random integer in range 1 to sum of integers below and pick a move from particular bucket.

• join_by_advice_p=number
• extend_p=number
• disconnect_p=number
• interchange_p=number
• local_p=number

Read set configuration

• type=read type Required. Can be "single", "paired" or "pacbio".
• filename=filename Required for single and pacbio reads. Filename where your reads are. Must be in fastq format.
• filename1=filename Required for paired reads. Filename where one end of your paired reads are. Must be in fastq format and reads are assumed to be innies.
• filename2=filename Required for paired reads. Filename where the other end of your paired reads are. Must be in fastq format and reads are assumed to be innies.
• insert_mean=number Required for paired reads. Mean insert length for paired reads.
• insert_std=number Required for paired reads. Standard deviation of the insert length for paired reads.
• cache_prefix=path Optional. Where to put cached data from likelihood calculation. Defaults to read set name.
• weight=number Optional. Weight of the read set in the likelihood calculation. Default 1.
• advice=whatever Optional. If set then we use this read set as advice during walk extending.
• mismatch_prob=number Optional. Probablity of errors in your reads. Defaults to 0.01.
• min_prob_start=number Optional. Constant c in the minimum probablity calculation. Defaults to -10.
• min_prob_per_base=number Optional. Constant k in the minimum probablity calculation. Defaults to -0.7.
• penalty_constant=nubmer Optional. Alpha constant in penalty for assemblies which are not connected enough.
• penalty_step=number Optional. Constant k in penalty for assemblies which are not connected enough.

Source code organization

• gaml.cc - main file, contains optimization routine and functions for loading configuration
• moves.cc, moves.h - contain source code for all moves
• graph.cc, graph.h - contain code for manipulation with assembly graph and calculating likelihood for one read set
• input_output.cc, input_output.h - routines for assembly output and debug output
• prob_calculator.h - class for calculating whole assembly likelihood