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hiraksarkar authored Feb 8, 2019
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[![Build Status](https://travis-ci.org/COMBINE-lab/minnow.svg?branch=master)](https://travis-ci.org/COMBINE-lab/minnow)
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# Minnow ( read level simulator for dscRNA-seq data)


Most analysis pipelines validate their results using known marker genes (which are not widely available for all types of analysis) and by using simulated data from gene-count-level simulators. Typically, the impact of using different read-alignment or UMI deduplication methods has not been widely explored. Assessments based on simulation tend to start at the level of assuming a simulated count matrix, ignoring the effect that different approaches for resolving UMI counts from the raw read data may produce. Here, we present minnow, a comprehensive sequence-level droplet-based single-cell RNA-seq (dscRNA-seq) experiment simulation framework. Minnow accounts for important sequence-level characteristics of experimental scRNA-seq datasets and models effects such as PCR amplification, CB (cellular barcodes) and UMI (Unique Molecule Identifiers) selection, and sequence fragmentation and sequencing.

Minnow is a read level simulator for droplet based single cell RNA-seq data. Minnow simulates the reads by sampling sequences from the underlying de-Bruijn graph (using `--dbg`) of the reference transcriptome or alternatively just samples sequences from the reference transcriptome. As the `--dbg` option also enables other features of the software, it is useful to describe those.
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