sequenceprofiler

• This crate has the following features: fasta file should be a linear fasta and not a multi line fasta just like long-read.

• 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.

• 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

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sequenceprofiler
  ************************************************
  Author Gaurav Sablok,
  Email: codeprog@icloud.com
  ************************************************

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

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

• To install windows version:

rustup component add llvm-tools
rustup target add x86_64-pc-windows-msvc
git clone https://github.com/IBCHgenomic/ensemblcov.git
cd ensemblcov
cargo xwin build --target x86_64-pc-windows-msvc

Gaurav Sablok
codeprog@icloud.com