Metadata-Version: 2.1
Name: covviz
Version: 1.0.3
Summary: Multi-sample coverage browser
Home-page: https://github.com/brwnj/covviz
Author: Joe Brown
Author-email: brwnjm@gmail.com
License: UNKNOWN
Description: 
        # covviz
        
        Coverage visualization; a companion viewer for indexcov results.
        
        Here we use [indexcov](https://github.com/brentp/goleft/tree/master/indexcov)
        to quickly estimate the coverage across samples then find regions of large,
        coverage-based anomalies. The aim is to highlight regions of significant
        (passing the user's z-score threshold) and sustained (beyond user specified
        distance) deviation from the majority of samples. Significance is determined
        using z-scores (`--zthreshold`) for all samples at all points using median
        absolute deviation, but in order to be highlighted, points must be significant
        consecutively throughout a user specified distance (`--distancethreshold`).
        
        # Usage
        
        Install `nextflow`:
        
        ```
        curl -s https://get.nextflow.io | bash
        ```
        
        Full nextflow installation instructions are available at:
        https://www.nextflow.io/
        
        To simplify prerequisite software installations and software version tracking,
        we strongly recommend running `covviz` using Docker or Singularity. Docker
        installation instructions for your operating system are available at:
        https://docs.docker.com/install/
        
        Then, with Docker or Singularity we run:
        
        ```
        nextflow run brwnj/covviz -latest -profile docker \
            --indexes 'data/indexes/*.crai' \
            --fai data/g1k_v37_decoy.fa.fai \
            --gff data/Homo_sapiens.GRCh37.82.gff3.gz
        ```
        
        Which gives us `./results/covviz_report.html`.
        
        ## Required arguments
        
        + `--indexes`
            + quoted file path with wildcard ('*.crai') to cram or bam indexes
        + `--fai`
            + file path to .fai reference index
        + `--gff`
            + file path to gff matching genome build of `--indexes`
        
        ## Options
        
        + `--outdir`
            + output directory for results
            + default: "./results"
        + `--sexchroms`
            + sex chromosomes as they are in `--indexes`
            + default: "X,Y"
        + `--exclude`
            + regular expression of chromosomes to skip
            + default: "^GL|^hs|^chrEBV$|M$|MT$|^NC|_random$|Un_|^HLA\\-|_alt$|hap\\d+$"
        + `--zthreshold`
            + a sample must greater than this many standard deviations in order to be found significant
            + default: 3.5
        + `--distancethreshold`
            + consecutive significant points must span this distance in order to pass this filter
            + default: 150000
        + `--slop`
            + leading and trailing segments added to significant regions to make them more visible
            + default: 500000
        + `--project`
            + can be used to name your indexcov to something more meaningful
            + default: "NF"
        
        
        # Report
        
        ## Interactive example
        
        See: https://brwnj.github.io/covviz/
        
        ## Scaled chromosome coverage
        
        Significant regions will be displayed in color atop a gray region which represents the upper and lower bounds of a given point minus any values deemed significant.
        
        ![significant_regions](data/img/significant_regions.png)
        
        ## Proportions covered
        
        ![proportional_coverage](data/img/proportional_coverage.png)
        
        The metadata table will be displayed below the plots.
        
        ## Interaction
        
        Clicking on plot traces highlights the line and searches the metadata. Double-clicking de-selects lines, resets the plot, and de-selects samples from the table. Clicking on the gene track launches a search for the gene's respective Gene Card. In cases where genes overlap, multiple windows/tabs will be opened.
        
        # License
        
        covviz is free and unrestricted for non-commercial use. For commercial use,
        please contact [bpedersen@base2genomics.com].
        
Platform: UNKNOWN
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: Implementation :: PyPy
Requires-Python: >=3.6.0
Description-Content-Type: text/markdown
