graph-kmers

• rust graph kmers which allows based on the similarity of the shared unique kmers filtering of the sequences so that you can build anative index faster graph.

cargo build 

12:33:48 gauravsablok@genome graph-kmer main ? ./target/debug/graph-kmers -h
graphkmers

Usage: graph-kmers <COMMAND>

Commands:
 sequence  identity kmer similarity index
 filter    identity kmer filter
 help      Print this message or the help of the given subcommand(s)

Options:
 -h, --help     Print help
 -V, --version  Print version
12:33:53 gauravsablok@genome graph-kmer main ? ./target/debug/graph-kmers sequence -h
identity kmer similarity index

Usage: graph-kmers sequence <SEQUENCEPATH> <SEQUENCEKMER>

Arguments:
 <SEQUENCEPATH>  provide the path to sequence file
 <SEQUENCEKMER>  provide the kmer to be profiled for the sequence similarity

Options:
 -h, --help  Print help
12:33:57 gauravsablok@genome graph-kmer main ? ./target/debug/graph-kmers filter -h
identity kmer filter

Usage: graph-kmers filter <SEQUENCE> <KMER> <THRESHOLD>

Arguments:
 <SEQUENCE>   provide the path to the sequence file
 <KMER>       sequence kmer for the identity kmer
 <THRESHOLD>  provide the threshold

Options:
 -h, --help  Print help

• to run the compiled library

12:53:04 gauravsablok@genome graph-kmer main ? \ 
          ./target/debug/graph-kmers filter \
                          ./samplefile/sample.fasta 4 10

12:56:27 gauravsablok@genome samplefile main ? 
          ./target/debug/graph-kmers sequence 
                         ./samplefile/sample.fasta 4


12:55:34 gauravsablok@genome samplefile main ? head -n 4 frequencies-t*
==> frequencies-tab.txt <== filtering without the threshold
"chr11:66478458"        "chr11:66478459"        22      44      50.0
"chr11:66478458"        "chr11:66478460"        12      44      27.272728
"chr11:66478458"        "chr11:66478461"        8       42      19.047619
"chr11:66478458"        "chr11:66478462"        9       41      21.95122

==> frequencies-threshold.txt <== filtering after the threshold
"chr11:66478458"        "chr11:66478459"        22      44      50.0
"chr11:66478458"        "chr11:66478460"        12      44      27.272728
"chr11:66478458"        "chr11:66478461"        8       42      19.047619
"chr11:66478458"        "chr11:66478462"        9       41      21.95122

Gaurav Sablok