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cosmo-team / cosmo-issues

Issue repository for Cosmo (separate until we can transfer issues between repositories nicely - ignore code)
http://www.github.com/cosmo-team/cosmo
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Support output from BCALM #22

Open alexbowe opened 10 years ago

alexbowe commented 10 years ago

BCALM outputs the simple paths, which means only one of each kmer (not its reverse complement). This should make our graph smaller.

alexbowe commented 10 years ago

This would involve extracting all kmers, then running the packer without adding reverse complements. Could be prototyped easily with a Python tool, but eventually might want to make the reverse complements thing a dynamic flag.

Worth testing without BCALM, since it should be faster (all in memory).

alexbowe commented 8 years ago

Closing this, since bcalm output is ascii and can easily be converted to a fasta file.

alexbowe commented 8 years ago

Reopening as latest BCALM may have different format, + we don't accept any ascii input anyway (+ need flag to disable adding revcomps)

alexbowe commented 8 years ago

Additionally, using STXXL + sorting + set differences, may be possible to implement simple BCALM-like implementation where the minimizers are of k-1 (node) length (which would be worth comparing to BCALM).