Example Files

Amplicon Analysis

Sample SMRTpipe parameter file (no barcoding)

<?xml version="1.0"?>
<smrtpipeSettings>
    <module name="P_Fetch"/>
    <module name="P_Filter"/>
    <module name="P_AmpliconAssembly">
        <param name="maxReads">         
            <value>2000</value>
        </param>
        <param name="maxPhasingReads">  
            <value>500</value>
        </param>
        <param name="minLength">        
            <value>3300</value>
        </param>
        <param name="minSnr">           
            <value>4.0</value>
        </param>
    </module>
</smrtpipeSettings>

Sample SMRTpipe parameter file (barcoded)

<?xml version="1.0"?>
<smrtpipeSettings>
    <module name="P_Fetch"/>
    <module name="P_Filter"/>
    <module name="P_Barcode">
        <param name="barcode.fasta">    
            <value>/path/to/barcode/fasta</value>
        </param>
        <param name="mode">             
            <value>paired</value>
        </param>
        <param name="adapterSidePad">   
            <value>5</value>
        </param>
        <param name="insertSidePad">    
            <value>0</value>
        </param>
    </module>
    <module name="P_AmpliconAssembly">
        <param name="maxReads">         
            <value>2000</value>
        </param>
        <param name="maxPhasingReads">  
            <value>500</value>
        </param>
        <param name="minLength">        
            <value>3000</value>
        </param>
        <param name="minSnr">           
            <value>4.0</value>
        </param>
    </module>
</smrtpipeSettings>

Sample SMRTanalysis Shell script (no barcoding)

WARNING: This script assumes you are working from a computing cluster with 16-processors and at least 4 GB of RAM.

export  SMRT=~/builds/smrtanalysis-2.2.0
export  INPUT=non_barcoded_input.fofn
export  OUTPUT=non_barcoded_output
source  $SMRT/etc/setup.sh
ConsensusTools.sh  AmpliconAssembly  --maxReads 2000                 \
                                     --minLength 3000                \
                                     --minSnr 4.0                    \
                                     --output $OUTPUT                \
                                     --numThreads 15                 \
                                     --fofn $INPUT                   \

Sample SMRTanalysis Shell script (barcoded)

WARNING: This script assumes you are working from a computing cluster with 16-processors and at least 4 GB of RAM.

export  SMRT=~/builds/smrtanalysis-2.2.0
export  INPUT=barcoded_input.fofn
export  OUTPUT=barcoded_output
export  BARCODES=barcodes.fasta
export  BARCODE_OUTPUT=barcoded_input_barcoding
export  BARCODE_FOFN=barcoded_input_barcoding.fofn
source  $SMRT/etc/setup.sh
mkdir   $BARCODE_OUTPUT
pbbarcode  labelZmws  $BARCODES                                      \
                      $INPUT                                         \
                      --nProcs 15                                    \
                      --adapterSidePad 5                             \
                      --insertSidePad 0                              \
                      --scoreMode paired                             \
                      --outDir $BARCODE_OUTPUT                       \
                      --outFofn $BARCODE_FOFN                            
ConsensusTools.sh  AmpliconAssembly  --maxReads 2000                 \
                                     --minLength 3000                \
                                     --barcodes $BARCODE_FOFN        \
                                     --output $OUTPUT                \
                                     --numThreads 15                 \
                                     --fofn $INPUT                   \