Please note that this mode has been removed from Goby 2.0. Simply use an aligner with Goby support instead.

This mode is used to run third party aligners, taking care of data translations. Data translations include converting compact reads to the aligner input and converting the aligner output to compact alignment format. It is implemented by edu.cornell.med.icb.goby.modes.AlignMode.java.

Mode Parameters

The following options are available in this mode

FlagArgumentsRequiredDescription
(-r|--reads)readsnoName of the compact reads input file. Required to –search.
(-d|--reference)referenceyesName of the compact reads reference file, or path to the formatted database previously produced with the –index option.
(-f|--read-index-filter)read-index-filternoThe name of a read index filter. When provided, the aligner will only be provided with the reads that are included in the filter.
(-g|--reference-index-filter)reference-index-filternoThe name of a reference index filter. When provided, the aligner will only search references whose indices are included in the filter.
--work-directorywork-directorynoThe work directory.
--database-directorydatabase-directorynoThe database directory.
--database-namedatabase-namenoThe database name.
--searchn/anoWhen this switch is provided, search the reads against the reference.
--indexn/anoWhen this switch is provided, index the reference. Name the indexed reference according to the output basename. Indexing is done as part of search when it is required by the aligner, but this option is provided to build an aligner index independently from a search.
--keep-temporary-filesn/anoWhen this switch is provided, keep temporary files created during the alignment. These files typically hold the result of the alignment in the native aligner format.
--get-default-database-namen/anoWhen this switch is provided, the default database name for the specified –reference file will be returned on stdout.
(-a|--aligner)aligneryesName of the third-party aligner to align with. Must one of {bwa,last,lastag}.
(-o|--options)optionsnoAligner specific options. Specifying “–options m=3,k=2” will pass the string “-m 3 -k 2” to the aligner. Supports any options that are supported by the aligner.
--color-spacen/anoWhen this switch is provided, convert the sequence to color mode. Only makes sense if the compact file encodes a sequence in fasta format.
(-p|--quality-filter-parameters)quality-filter-parametersyesParameters to configure the quality filter. [“quality-filter-parameters” and “ambiguity-threshold” may eventually be condensed into “filterOptions”]
--ambiguity-thresholdambiguity-thresholdnoMaximum number of locations that a read can match to be included in the alignment entries. [“quality-filter-parameters” and “ambiguity-threshold” may eventually be condensed into “filterOptions”]
(-b|--basename)basenamenoBasename of the alignment to output.