ARC (Assembly by Reduced Complexity)
- 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.
- 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
- 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.