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  1. Comparing and evaluating assembly with graph alignment

    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 ...

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  2. Labeling a sparse covering of a De Bruijn graph, and utility thereof

    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 ...

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  3. Abundance counting of sequences in graphs with graphalign

    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 ...

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