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Align Reads using TopHat2 - v1.0.1


By: tgu2


Align sequencing reads to a reference genome using TopHat2 to identify exon-exon splice junctions.

This App aligns the sequencing reads for a set of two or more samples to a genome using TopHat2 in order to identify splice junctions between exons with the help of Bowtie2 mapping program. Alternatively, if the user has only a single sample of reads or set of reads, this App will take single-end or paired-end library object or reads set instead of a sample set.

In addition, it outputs the Qualimap generated BAM alignment QC report that includes global summary such as total number of mapped reads, mean samples coverage, mean samples GC-content, mean samples mapping quality, and sample statistics for each sample along with PCA and coverage statistics in histograms.

NOTE: This method is one of the steps of the KBase RNA-seq Pipeline , however it can also be run standalone for one or more samples.

Team members who developed & deployed algorithm in KBase: Tianhao Gu, Christopher Henry, Shane Canon, Stephen Chan, Jason Baumohl, Sean McCorkle, Sunita Kumari, Shinjae Yoo, Priya Ranjan, Vivek Kumar

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App Specification:

Module Commit: ca4e61a397646dd2a4051f1e59de22dc95d1eed1