demogenas

democratizing genome assembly

Usage:

You are going to need at least 2 file:

data file - a tab delimited file specifying the location and type of data for your samples (example: data/testdata/test.data.tsv)
config file - specifying parameters for the pipeline (example: data/testdata/test.config.yaml)

The example data file (data/testdata/test.data.tsv) specifies 5 hypothetical samples comprising different kinds of input data:

fastq_only - a sample for which multiple libraries were sequenced and all data come in fastq format
bam_only - a sample for which multiple libraries were sequenced and all data come in bam format
fastq_bam - a sample for which multiple libraries were sequenced and data come as fastq and bam format
fast5_only - a sample for which multiple libraries were sequenced and data comes as fast5
all_types - a sample for which multiple libraries were sequenced and data come in fastq, bam and fast5 format

Per default, demogenas will process (trim, errorcorrect, merge) and assemble all samples and datatypes in the datafile automatically, with the particular steps (trimmers, correctors, assemblers) as specified in the config file.

./demogenas -t local -m assemble --configfile=data/testdata/test.config.yaml --dry

If you want to process only selected samples in the data file you can specify the sample(s) of interest with the --select= option, e.g.:

# assemble one sample 'fastq_only'
./demogenas -t local -m assemble --configfile=data/testdata/test.config.yaml --dry --select=fastq_only

# assemble two samples 'fastq_only' and 'bam_only'
./demogenas -t local -m assemble --configfile=data/testdata/test.config.yaml --dry --select=fastq_only,bam_only

You can check the different behaviours of the pipeline for different sample/data types - note that demogenas will do different things depending on the data types provided, e.g.:

# only fastq
./demogenas -t local -m assemble --configfile=data/testdata/test.config.yaml --dry --select=fastq_only
# only bam
./demogenas -t local -m assemble --configfile=data/testdata/test.config.yaml --dry --select=bam_only
# combination of fastq and bam
./demogenas -t local -m assemble --configfile=data/testdata/test.config.yaml --dry --select=fastq_bam
# fast5 only
./demogenas -t local -m assemble --configfile=data/testdata/test.config.yaml --dry --select=fast5_only
# combination of fastq, bam and fast5
./demogenas -t local -m assemble --configfile=data/testdata/test.config.yaml --dry --select=all_types

Via the config file I control which steps are performed, e.g.:

# process illumina data and assemble with all relevant assemblers
./demogenas -t local -m assemble --configfile=data/testdata/test.config.yaml --dry --select=fastq_only
# process illumina data and assemble only with spades
./demogenas -t local -m assemble --configfile=data/testdata/test.config.spadesonly.yaml --dry --select=fastq_only

If you don't want to go all the way and assemble, there are other modes, such as:

-m trim_illumina
-m correct_illumina
-m merge_illumina
-m eval_illumina

# trim illumina data
./demogenas -t local -m trim_illumina --configfile=data/testdata/test.config.yaml --dry --select=fastq_only
# trim illumina data and evaluate (fastqc, kmer spectrum)
./demogenas -t local -m eval_illumina --configfile=data/testdata/test.config.yaml --dry --select=bam_only
# trim and correct illumina data
./demogenas -t local -m correct_illumina --configfile=data/testdata/test.config.yaml --dry --select=fastq_bam
# trim, correct and merge illumina dat
./demogenas -t local -m merge_illumina --configfile=data/testdata/test.config.yaml --dry --select=fastq_only

Note that for a sample comprising only fast5 data none of the illumina specific steps will be done. You can try.

./demogenas -t local -m trim_illumina --configfile=data/testdata/test.config.yaml --dry --select=fast5_only
./demogenas -t local -m correct_illumina --configfile=data/testdata/test.config.yaml --dry --select=fast5_only
./demogenas -t local -m merge_illumina --configfile=data/testdata/test.config.yaml --dry --select=fast5_only

We have extra modes to evaluate your assemblies - this can be done at any time, even if not all assemblies are finished yet.

First, run prepare_assmblies mode - this will gather all assemblies that are finished at this stage.

./demogenas -m prepare_assemblies -t local --configfile=data/testdata/test.config.yaml --select="fastq_only"

Now, to evaluate with the methods as specified in the config file, run evaluate_assemblies like e.g. so:

./demogenas -m evaluate_assemblies -t local --configfile=data/testdata/test.config.yaml --select="fastq_only"

reslp/demogenas

demogenas