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Assembly by Reduced Complexity (ARC)
Python R Shell

ARC (Assembly by Reduced Complexity)

For details about ARC installation, usage, and output, please visit the ARC web page:


ARC Updates:


  • 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.


  • 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.


  • 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.



  • 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.


  • 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.
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