Zenodo release

Stable release of nPhase for archival by Zenodo

Stable release

This version mainly includes the new raw result cleaning step and some minor improvements (checking if the reference is already indexed, using multiple threads for steps like short read mapping).

Stable release

Fixed length 0 cluster issue

Fixed a bug that was introduced by the previous update

Stable release

Fixed Issue #4
Fixed bug with bwa mem not running properly on MAC OS devices (Issues defining tab characters for the RG field, fixed by using Picard to add an RG field after mapping with bwa mem)

Changed cluster and read naming conventions to better handle introspective analyses

Changed version of plotnine to >=0.7.1 to fix issues with facet_wrap function
Changed the x axis for the phased plots for better readability
Added coverage calculation using a 10kb window and visualization using plotnine
Added discordance (allele frequency within each cluster) calculation and visualization using plotnine
Added filtering method that generates a filtered coverage file, keeping only reads within the top 95% most highly covered reads (Potentially wasn't a good implementation)
Started laying the groundwork for an nphase filtering method, still incomplete.

Stable release

Latest bugfixes, small change to the generated plot to make it look more like the paper.

Please install using

conda install -c oakheart nphase

And update using

conda update -c oakheart nphase

It should be quick and painless and this way all the dependencies are taken care of. Only clone the repo and install its pre-requisites manually if you know exactly what you're doing.

Stable release

This new release fixed some bugs present in the bioRxiv release (high base quality errors and a fastQ file formation error) and now includes an example test set.

Still recommend installing through

conda install -c oakheart nphase

But you may want to get this in order to test the tool on the example data.

biorXiv release

This is the release at the time of pre-publishing in biorXiv (https://www.biorxiv.org/content/10.1101/2020.07.24.219105v1).

Though please install using

conda install -c oakheart nphase

It should be quick and painless and this way all the dependencies are taken care of. Only clone the repo and install its pre-requisites manually if you know what you're doing.