collapse-duplication collapses output from heatitup and heatitup-complete
into clones by looking at the positions of their duplications and spacers.
There are three related tools for this program:
-
heatitupto categorize longest repeated substrings along with characterizing the “spacer” in-between substrings. -
heatitup-completeto applyheatituptoBAMfiles along with additional options for preprocessing. -
collapse-duplicationto collapse annotated reads found byheatitupinto clones with associated frequencies.
See https://docs.haskellstack.org/en/stable/README/ for more details.
curl -sSL https://get.haskellstack.org/ | sh
stack setupstack install collapse-duplicationstack installHere, heatitup_output.csv must have a label field with the format SUBJECT_SAMPLE.
cat heatitup_output.csv | collapse-duplication --wiggle 5 --filterCloneFrequency 0.01 --collapseClonecollapse-duplication, Gregory W. Schwartz. Collapse the duplication output into
clones and return their frequencies or clone IDs. Make sure format of the label
field is SUBJECT_SAMPLE
Usage: collapse-duplication [--output STRING] [--collapseClone]
[--wiggle DOUBLE] --filterCloneFrequency DOUBLE
[--filterReadFrequency DOUBLE] [--absolute]
[--filterType STRING] [--method STRING]
Available options:
-h,--help Show this help text
--output STRING (FILE) The output file.
--collapseClone Collapse the clone into a representative sequence
instead of appending clone IDs to the reads.
--wiggle DOUBLE ([0] | DOUBLE) Highly recommended to play around
with! The amount of wiggle room for defining clones.
Instead of grouping exactly by same duplication and
spacer location and length, allow for a position
distance of this much (so no two reads have a
difference of more than this number).
--filterCloneFrequency DOUBLE
([0.01] | DOUBLE) Filter reads (or clones) from
clones with too low a frequency. Default is 0.01
(1%).
--filterReadFrequency DOUBLE
([Nothing] | DOUBLE) Filter duplications with too
high a frequency (probably false positive if very
high, for instance if over half of reads or 0.5).
Converts these duplications to "Normal" sequences.
Frequencies and counts are taken place before
collapsing and filtering.
--absolute Whether to filter reads (or clones) from clones with
too low an absolute number for filterReadFrequency
instead frequency.
--filterType STRING ([Substring] | Position) Whether to filter reads with
filterReadFrequency using the dSubstring field or the
dLocations field.
--method STRING ([CompareAll] | Hierarchical) The method used to
group together wiggle room reads. Compare all
compares the current element with all elements in the
previous sublist. Hierarchical is for clustering, but
is most likely worse at this point in time.