sequenceprofiler

• This crate has the following features:
• Sequence, which allows based on the similarity of the shared unique kmers and also allows for the filtering of the sequences so that you can build a native index graph faster.
• SequenceSeq, which allows for the sequence similarity on a sequence to next iter sequence.
• longread: finding the origin of the kmers.Back to sequences:Find the origin of 𝑘-mers DOI: 10.21105/joss.07066. Output a table for the direct ingestion into any graphs. Outputs a sam type file with the distinct count of the kmers and can be used for the jellyfish count.Support both the genome and the longread fasta file. genome fasta file should be a linear fasta and not a multi line fasta just like long-read.
• Jellyfish: a rust implementation of the jellyfish for the counts.Outputs both the unique counts, all counts.It will produce allkmers, uniquekmers, countkmers

cargo build 

gauravsablok@genome graph-kmer main ? ./target/debug/sequenceprofiler
sequenceprofiler

Usage: sequenceprofiler <COMMAND>

Commands:
 sequence      identity kmer similarity index
 filter        identity kmer filter
 sequence-seq  compare seq to other seq 1-1 iteration
 jellyfish     jellyfish counter for the long reads
 origin-kmer   finding the origin of kmers
 help          Print this message or the help of the given subcommand(s)

Options:
 -h, --help     Print help
 -V, --version  Print version 

• to run the compiled library

./target/debug/sequenceprofiler sequence
    ./samplefile/sequence-sample-files/sample.fasta 4
./target/debug/sequenceprofiler filter
      ./samplefile/sequence-sample-files/sample.fasta 4 10  
./target/debug/sequenceprofiler origin-kmer
          ./samplefile/longread-sample-files/fastafile.fasta 4
./target/debug/sequenceprofiler jellyfish
         ./samplefile/jellyfish-sample-files/test.fastq 4````

Gaurav Sablok