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Michal Stolarczyk

Username    michalstolarczyk
Date joined   Joined

22 projects

refgenie

Last released

Refgenie creates a standardized folder structure for reference genome files and indexes. You can download pre-built genomes or build your own for any fasta file

refgenconf

Last released

A standardized configuration object for reference genome assemblies

yacman

Last released

A standardized configuration object for reference genome assemblies

pipestat

Last released

A pipeline results reporter

bulker

Last released

Manager of portable multi-container computing environments

looper

Last released

A pipeline submission engine that parses sample inputs and submits pipelines for each sample.

refgenieserver

Last released

This server provides both a web interface and a RESTful API. Users may explore and download archived indexes from the web interface or develop tools that programmatically query the API.

eido

Last released

A project metadata validator

peppy

Last released

A python-based project metadata manager for portable encapsulated projects

bbconf

Last released

Configuration package for bedbase project

attmap

Last released

Multiple access patterns for key-value reference

ubiquerg

Last released

Various utility functions

geofetch

Last released

Downloads data and metadata from GEO and SRA and creates standard PEPs.

divvy

Last released

A python-based configuration manager for portable environment configurations

logmuse

Last released

Logging setup

loopercli

Last released

A pipeline submission engine that parses sample inputs and submits pipelines for each sample.

caravel

Last released

Caravel provides aweb interface to interact with your PEP-formatted projects. Caravel lets you submit jobs to any cluster resource manager, monitor jobs, summarize results, and browse project summary web pages.

lucidoc

Last released

API documentation in Markdown

veracitools

Last released

Testing utilities

piper

Last released

A lightweight python toolkit for gluing together restartable, robust command line pipelines

pararead

Last released

Parallel processing of sequencing reads

ngstk

Last released

Next-generation sequencing utility functions

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