ARC (Assembly by Reduced Complexity)

For details about ARC installation, usage, and output, please visit the ARC web page: http://ibest.github.io/ARC/.

News

ARC Updates:

2014-09-02:

• Released version v1.1.3 to reflect the following tweaks, improvements and bug fixes:
  • ARC no longer produces a "deprecated method" warning with Biopython v1.64
  • ARC now supports high-specificity mapping on iteration 1, set sloppymapping=False
  • ARC now supports doing work in a different folder, set workingdirectory='/path/to/fast/storage'
  • ARC now generates new summary tables named target_summary_table.tsv
  • ARC now supports simple-repeat-masking on iteration 1 when maskrepeats=True is set
  • ARC default max_incorporation now defaults to 10 instead of 5.

2014-08-21:

• Two exciting updates for ARC (in the develop branch):
  • ARC's behavior has been modified so that it will mask the reference sequences for simple repeats on iteration 1 if maskrepeats=True (the default).
  • A new summary table named "target_summary_table.tsv" is now generated which complements the information already reported in "mapping_stats.tsv".
    • This file is created for each sample, and contains target specific details for every target in the original set of reference sequences.
    • Targets can have one of the following statuses:
      • NoReads - no reads were recruited by this target
      • Finished - target was finished normally
      • Killed - Assembly time was longer than assemblytimeout
      • Repeat - target recruited too many reads and may be a repeat
• It was found that the default max_incorporation=5 repeat detection setting was too aggressive in cases where divergent references were used. The default for this setting has been adjusted to a more conservative max_incorporation=10.

2014-07-28:

• ARC (develop branch) now has a "sloppymapping" parameter which can be used to turn off the low-specificity mapping on iteration 1. This works with both Bowtie2 and BLAT.

2014-07-24:

• ARC has a web page: http://ibest.github.io/ARC/
• ARC has a Google Group: https://groups.google.com/forum/?hl=en#!forum/arc-assembly

2014-03-12:

• Some major improvements were made over the last few months, these include:
  • A total refactor of the job handling mechanism which improved efficiency and speed, and simplified the code significantly.
  • A bug was identified in the code which would allow bowtie2 to map a read to more than one target even when bowtie_2k=1 was set (in certain circumstances). This should be resolved now, but more testing wouldn't hurt.
  • Fixed a race condition which sometimes caused ARC to crash on slow file systems.
  • Version number is ALWAYS printed out to help with debugging.
  • The latest version should by v1.1.1. Upgrading to this version is recommended.

2014-01-10:

• Fixing the Git branches so that we have "master" and "develop" again.
• A variety of improvements and bug fixes which all seem to be working well.
• Prepping for a v1.1.0 release.