Mash

Mash is a fast genome and metagenome distance estimation tool based on MinHash sketches. In this module, Mash compares uploaded sequence files and generates pairwise distance estimates and a distance matrix.

Workflow

1. Input sequence files
   Upload at least two FASTA sequence files for comparison.

2. Build Mash sketches
   Generate MinHash sketches for the input sequence files.

3. Calculate pairwise distances
   Use Mash to estimate pairwise distances, p-values, and shared hash counts between all input files.

4. Generate distance matrix
   Convert pairwise comparison results into a symmetric distance matrix for downstream comparison or visualization.

Data

The Mash sample dataset uses two assembled FASTA files from sample ERR260162: ERR260162.scaffold_500bp.fa and ERR260162.scaftig.fa. These files are used to demonstrate sequence-level distance comparison between assembled scaffold and scaftig datasets.

Result

v0.2: The pipeline is stored in Code Repository: CRS1242269173246341120. The computational docker enrionment is stored in Software Repository: SRS1242275112972201984.

Reproducibility

The pipeline utilizes code CRS1242269173246341120 and Docker image SRS1242275112972201984, both of which are stored in the BMAP repositories.

Usage

1. Select the application 'Mash'
2. Click on the 'Analysis' button
3. Click on the 'Metagenomics pipeline'
4. Fill in the request parameters

5. Upload the compressed data in gz or rar format.