Arachne is now capable of utilizing transposon reads more effectively. Specifically, the information given in pairings of transposon reads is used, whereas transposon reads were treated as unpaired reads previously. Transposon pairs must be handled differently than other pairs because their relative orientation is reversed, i.e. they point away from each other instead of toward each other. To accommodate this, the meanings of the insert_size and insert_stdev fields of the traceinfo file format are used to indicate the estimated separation of the beginnings of the transposon reads, rather than the length of the insert itself, which for a transposon is effectively zero. Also, the template_id field is used to pair reads from each transposon event, requiring a unique value for each such event. This is a kludge that is likely to disappear in a future release.
To indicate that a given read pair is a transposon pair, the configuration file now allows the
type field to set to any of:
paired_production, unpaired_production, and
transposon. Note that reads typed as transposon,
like those typed as paired_production, must have non-empty template_id and trace_end fields and non-zero insert_size and insert_stdev fields.
New Assembly Options
Arachne now has a number of new options available which enable, disable, or adjust the use of algorithms detailed in our paper ("Whole-Genome Sequence Assembly for Mammalian Genomes: ARACHNE 2", Genome Research, January 2003).
See the Running Arachne section
of the manual for more information.
New Output Files and Formats
While the report (assembly.ps) remains largely unchanged from the
first release, the format of the assembly.reads and assembly.links files have
changed, and there is a new file, assembly.unplaced.
See the Output section of the manual for more information.
Also, the acefiles produced by Arachne now include the entire (untrimmed) set of bases of the reads, making it easier to use the corresponding phd files with consed. Note that the acefiles produced by Arachne have only been tested with versions 7.52 and 12 of consed and may not be compatible with other versions.
See the Generating ace files section of the manual for more information.