SSWSort 2 is provided as both a Rust library, which can be used as a dependency in other projects, and as an executable binary, which can be run via command-line and replaces SSWSORT. The following documentation discusses usage and outputs for the binary, sswsort. For information on the library, read the [Rust docs].

Classifies (or sorts) sequences (influenza, SARS-CoV-2, RSV) using presets or DBs and a query sequence (FASTA). The classification is a best match criterion, and ignores same-strand repeats. SSWSORT will reject sequences that are unexpectedly long, chimeric (optional), and beyond the scoring thresholds.

Uses striped Smith-Waterman to classify sequences into a simple compound type

Usage: sswsort [OPTIONS] <MODULE> <INPUT> [OUTPUT_FILE]

Arguments:
  <MODULE>       Name of the classification module
  <INPUT>        Path to nucleotide sequences to classify in either FASTA or `.tsv` format. If `.tsv` format is being used, the `--input-is-tsv` boolean flag must also be used
  [OUTPUT_FILE]  Name of the tab-separated-value file for classifier results. If none are provided, STDOUT is used. If a directory is specified, a default filename of `sswsort_output.tsv`

Options:
      --input-is-tsv               Boolean flag for if the input provided is in TSV format instead of FASTA format
  -T, --threads <THREADS>       Number of threads to use. Defaults to number of physical cores otherwise
  -G, --is-grid-task            Execute as a partitioned task in a grid job, for use with: --submit-grid-job
  -S, --submit-grid-job <SIZE>  Submits and blocks on a grid job of the specified array size
  -h, --help                    Print help (see more with '--help')
  -V, --version                 Print version

./sswsort flu sswsort_res/flu.fasta
./sswsort cov-beta sswsort_res/cov-beta.fasta
./sswsort rsv sswsort_res/rsv.fasta

Clone this repo and, optionally, check out the latest release tag. You must install Rust nightly as a pre-requisite. You can then simply run the installer script:

./install.sh

1. Download the latest archive via our releases page for your target platform.
2. Unzip the archive containing sswsort.
3. Move the package to your desired location and add the folder to your PATH
   • Note: sswsort_res and sswsort must be in the same folder.

Simply run:

## From Github Container Repo
docker run --rm -itv $(pwd):/data ghcr.io/cdcgov/sswsort:latest sswsort # more args

SSWSORT expects input via a path to data in either FASTA format or TSV. Data may also be piped directly into the program. If using a TSV input, the --input-is-tsv boolean flag must also be used.

Example:

sswsort flu flu_samples.tsv --input-is-tsv

The TSV format should have the name/id of the read in the first column, followed by the sequence in the second column. Additional columns are allowed but ignored.

SSWSORT will provide output in a tab-separated format, with columns representing:

Program version, Reference module, Query name, Primary classified taxon, Primary classification score, Sequence length, Primary strand, Secondary classified taxon, Secondary score, Secondary strand

To receive a classification, the query must align with one of the reference sequences with a score greater than or equal to the score_minimum, or a normalized score greater than or equal to the norm_score_minimum, equal to the score divided by the length of the query. These parameters have default values that can be changed in the config.toml.

Classifications fall into the following categories:

SSWSORT utilizes a Striped Smith-Waterman alignment algorithm to align each query sequence to a list of references before classifying the query with the reference taxa that had the highest alignment score. The alignment uses these default following weights for scoring:

Defaults can be overridden at a module level within the config.toml.

Example:

[[classification_module]]
name = "flu"
version = "2.0"
alternative_names = []
norm_score_minimum = 1.0
score_minimum = 100
length_minimum = 25
reference_sequences = "flu.fasta"
detect_chimera = true
weights = { gap_open = -11, gap_extend = -2, mismatch = -3, match_weight = 1 }

will override the values for all weights. Note if some but not all weights are being overridden, the other values still need to be included in the toml.

Ambiguous nucleotides (N) and unrecognized characters are treated as 0-penalty mismatches. So, a query with one or more N bases will align with an identical score as a query with those bases missing.

Leading and trailing N's in a query sequence are removed prior to alignment. This will not affect the alignment score, but will affect the sequence length in the output, as well as the normalized score, which uses the edited length.

For direct correspondence on the project, feel free to contact: Samuel S. Shepard, Centers for Disease Control and Prevention or reach out to other contributors.

This repository constitutes a work of the United States Government and is not subject to domestic copyright protection under 17 USC § 105. This repository is in the public domain within the United States, and copyright and related rights in the work worldwide are waived through the CC0 1.0 Universal public domain dedication. All contributions to this repository will be released under the CC0 dedication. By submitting a pull request you are agreeing to comply with this waiver of copyright interest.

The repository utilizes code licensed under the terms of the Apache Software License and therefore is licensed under ASL v2 or later. This source code in this repository is free: you can redistribute it and/or modify it under the terms of the Apache Software License version 2, or (at your option) any later version. This source code in this repository is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache Software License for more details. You should have received a copy of the Apache Software License along with this program. If not, see: http://www.apache.org/licenses/LICENSE-2.0.html. The source code forked from other open source projects will inherit its license.

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