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marekkokot edited this page Oct 14, 2024 · 1 revision

The easiest way to get SPLASH is to use precompiled release. For innstance, to get 2.6.1 revision, please run the following command:

curl -L https://github.com/refresh-bio/SPLASH/releases/download/v2.6.1/splash-2.6.1.linux.x64.tar.gz

Then, one can perform an example analysis on the data from viral RNA sequencing. The data consists of four Illumina NovaSeq 6000 runs from the study entitled "Detection and prevalence of SARS-CoV-2 co-infections during the Omicron variant circulation":

cd example
./download.py #download examplary data
splash input.txt #run the pipeline with default parameters

The result consists of two TSV files, namely,

  1. result.after_correction.all_anchors.tsv
  2. result.after_correction.scores.tsv The first file contain all unfiltered anchors found by the pipeline. The second file contains only anchors whose corrected p-value is below 0.05.

Table of contents

Home

  1. Quick start
  2. Installation
    1. Precompiled binaries
    2. Docker container
    3. Singularity container
    4. Compile from sources
    5. Running the example
  3. Configuration
    1. Base configuration
    2. Filters and thresholds
    3. Additional output configuration
    4. Tuning statistics computation
    5. Technical and performance-related
    6. 10x or visium processing
  1. Input and output
    1. Input format
    2. Understanding the output
    3. Additional output
  2. Compactors
    1. Installation
    2. Toy examples
    3. Parameters
  3. Lookup table
    1. General idea
    2. Building the index
    3. Querying the index
    4. Extension
    5. Using transcriptomes files
    6. Supported input formats for a query
    7. Formatting the output
    8. Canonical k-mers
  4. Applications and results interpretation
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