One of our long-term interests has been in figuring out what the
!$!$!#!#%! assemblers actually do to real data, given all their
heuristics. A continuing challenge in this space is that short-read
assemblers deal with really large amounts of noisy data, and it can
be extremely hard to look at assembly ...
So far, in this week of khmer blog posts (1, 2, 3), we've been
focusing on the read-to-graph aligner ("graphalign"), which enables
sequence alignments to a De Bruijn graph. One persistent challenge
with this functionality as introduced is that our De Bruijn graphs
nodes are anonymous, so we have ...
De Bruijn graph alignment should
also be useful for exploring concepts in transcriptomics/mRNAseq
expression. As with variant calling
graphalign can also be used to avoid the mapping step in
quantification; and, again, as with the variant calling approach, we
can do so by aligning our reference sequences to the ...
There's an interesting and intuitive connection between error
variant calling - if you can do one well, it lets you do (parts of)
the other well. In the previous blog post on
some new features in khmer, we introduced our new "graphalign"
functionality, that lets us align short ...
About a month ago, I took some time to try out Docker, a
container technology that lets you bundle together, distribute, and
execute applications in a lightweight Linux container. It seemed neat
but I didn't apply it to any real problems. (Heng Li also tried it
out, and came ...