Syotti 2 Early Access Beta

Installing

First, install the Rust. Then:

git submodule update --init
cargo build --release

This produces the binary to target/release/syotti2. If you want to install the program to $PATH, run cargo install --path .

Usage

Usage: syotti2 [OPTIONS] <COMMAND>

Commands:
  design    
  coverage  
  help      Print this message or the help of the given subcommand(s)

Options:
  -j, --threads <threads>  Number of threads to use [default: 8]
  -h, --help               Print help

Subcommand design

Usage: syotti2 design [OPTIONS] --targets <targets> --output <output>

Options:
  -j, --threads <threads>
          Number of threads to use [default: 8]
  -t, --targets <targets>
          Input FASTA or FASTQ file, possibly gzipped
  -o, --output <output>
          FASTA outputfile for the baits
  -L, --bait-len <bait-length>
          Bait length [default: 120]
  -d, --hamming-distance <hamming-distance>
          Maximum number of mismatches allowed in matching [default: 40]
  -g, --seed-len <seed-len>
          Length of seeds in matching [default: 20]
  -m, --minimizer-len <minimizer-len>
          Length of minimizers in indexing. Must be less or equal to seed-len [default: 14]
  -c, --cutoff <cutoff>
          Stop the algorithm when this coverage fraction is reached [default: 1.0]
  -r, --randomize
          Randomize the processing order in the greedy algorithm
      --require-cutoff-for-every-sequence
          Stop only when every input sequence has reached the coverage cutoff individually
  -h, --help
          Print help

Subcommand coverage

Usage: syotti2 coverage [OPTIONS] --baits <baits> --targets <targets> --coverage-out <coverage-out>

Options:
  -b, --baits <baits>
          FASTA file containing the baits
  -j, --threads <threads>
          Number of threads to use [default: 8]
  -t, --targets <targets>
          FASTA or FASTQ file, possibly gzipped
  -d, --hamming-distance <hamming-distance>
          Maximum number of mismatches allowed in matching [default: 40]
  -g, --seed-len <seed-len>
          Length of seeds in matching [default: 20]
  -m, --minimizer-len <minimizer-len>
          Length of minimizers in indexing. Must be less or equal to seed-len [default: 14]
  -o, --coverage-out <coverage-out>
          Output csv file for the coverage data.
      --mismatch-out <mismatch-out>
          Output csv file for the mismatch data.
  -h, --help
          Print help (see more with '--help')

Subcommand coverage-picture

Visualize the coverage depth into a png image. Beware: the height is equal to the number of targets, and the width is equal to the length of the longest target. Use --resolution to reduce the width to avoid having an enormous image. To reduce the height, check out concat-into-rows.

Usage: syotti2 coverage-picture [OPTIONS]

Options:
  -i <infile>
          Input coverage file generated by the command --coverage
  -j, --threads <threads>
          Number of threads to use [default: 8]
  -o <outfile>
          Output png file for the coverage data.
      --concat-into-rows <concat-into-rows>
          Let the total number of bases be n, and let this parameter be r. Concatenates the coverage vectors and splits the concatenation into ceil(n/r) rows.
  -r, --resolution <resolution>
          Computes a moving average over the coverage vectors and samples those at evenly spaced intervals to get this many data points per sequence.
      --color-scale <color-scale>
          Sets the color mapping so that coverage of 'color-scale' and above map to maximum brightness. If not given, then the maximum coverage in the data is set to maximum brightness.
      --variable-resolution
          Relevant if --resolution is given. In enabled, makes it so that the resolution of each coverage vector is proportional to its length, such that the longest target has resolution equal to the value passed to --resolution. This is especially useful with --coverage-out-picture for better visualization.
  -h, --help
          Print help