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Old 06-18-2012, 06:55 AM   #1
Location: Tennessee

Join Date: Jun 2012
Posts: 10
Default ASAP: Advanced Sequence Automated Pipeline

Introducing ASAP: Advanced Sequencing Automated Pipeline
ASAP is an open source pipeline designed to assist users in managing various jobs associated with processing HiSeq data on a cluster or in serial.

The software is highly modular, so users can selectively use or skip any of the steps including:
  • Alignment with BWA
  • Local Realignment around known Variants with GATK
  • Quality score recalibration with GATK
  • SNP calls with Samtools, GATK, GlfMultiples or a consensus of 2 or more
  • INDEL calls with Samtools, GATK or a consensus
  • Annotation using ANNOVAR
  • Users can import bam files into a new or pre-existing pipeline and integrate those bams with bams created by ASAP for further processing (optional) and variant calls.

In addition to preparation, submission and monitoring of the processing scripts, ASAP also provides tools for slicing up fastq data for more parallel alignment, some basic QC including Ti/Tv ratios, heterozygous/homozygous alternate ratios, etc. to quickly identify issues before beginning analysis.

Data Integrity
To ensure only hi-quality data is used, a single job will fail if one of the child jobs fails or if quota issues prevent a successful copy. This means that no partially completed data slips through.

Software Download
Please feel free to have a look, and ask me any questions. The software can be freely downloaded at: There is a small tutorial with step by step instructions on how to use ASAP to install any missing components as well as run some data through the process.

Currently, ASAP is designed for paired-end sequence data from Illumina’s HiSEQ platform, but we are interested in working with other groups to make it work with other popular platforms as well. It should run on most (hopefully all) PBS and SGE clusters as well as in serial mode, however, it is possible to create support for other cluster systems.

Adding some new functionality, such as support for an alternate aligner or SNP caller should be relatively easy, but introducing entirely new functionality might require the knowledge of Ruby programming.
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Old 12-06-2012, 07:56 AM   #2
Location: Tennessee

Join Date: Jun 2012
Posts: 10
Default ASAP v1.1.4 Released

We have updated ASAP to version 1.1.4. Some features that have been added since the initial release include:
  • Support for processing single end reads (with bwa)
  • Bam Summaries with QPLOT
  • Optional support for GATK 2.x
  • Ability to automatically download most of the component applications, if they aren't already available
  • Many bug fixes and tweaks to make the software more user friendly and extendable.

We have posted a short tutorial on the website to allow users to try it out without spending too much time.

If you are tired of cobbling together dozens of scripts to create the jobs necessary to process your sequence data, digging through log files trying to identify which jobs failed due to a sick cluster node, or are just getting your first taste of sequence data, ASAP might prove to be a valuable time saver.
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Old 01-21-2013, 06:47 AM   #3
Location: Tennessee

Join Date: Jun 2012
Posts: 10
Default ASAP v1.1.7 Released

An updated version to ASAP has been released including a handful of bug fixes as well adding some features that might be of interest to users including:
  • Serial execution can now be run on multiple processors at once (this is in addition to the multithreaded options previously available). The number of jobs run at once is controlled by the user.
  • Batch Realignment now gives users control over how many samples to realign together, providing much faster realignment for large batches, while allowing the user to benefit from sharing information across samples.
  • Improved settings for baseline configurations with a focus on greater parallelizability.

The paper has also been published at BMC Research Notes:

Last edited by etorstenson; 07-22-2013 at 10:32 AM.
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Old 01-06-2016, 06:27 AM   #4
Location: Pakistan

Join Date: Oct 2015
Posts: 23

Hello etorstenson,

Unfortunately I am not being able to download it from the specified address which is So, can you kindly provide me working link. I want to try it out since I am new to NGS and i really like the pipeline specified. Thanks

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