- A kmer origin finding faster than the recent implementation of the recent implementation. 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
- crate is available at rust-genome-longread-count
Usage: kmerorigin <KMER_ARG> <FASTAFILE_ARG>
Arguments:
<KMER_ARG> please provide the kmer to be searched for the origin
<FASTAFILE_ARG> please provide the path to be searched for the strings containing the kmer
Options:
-h, --help Print help
-V, --version Print version
- a better table for direct ingestion into the graphs also to make a jellyfish count.
./target/debug/kmerorigin 4 ./sample-files/fastafile.fasta
>seq1
AGTCAGTC AGTC 0 4
AGTCAGTC GTCA 1 5
AGTCAGTC CAGT 3 7
AGTCAGTC TCAG 2 6
>seq2
AGGCAGTC CAGT 3 7
AGGCAGTC GGCA 1 5
AGGCAGTC AGGC 0 4
AGGCAGTC GCAG 2 6
Gaurav Sablok