BioMicroCenter:PPR Program: Difference between revisions
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<LI> PPR Program can be downloaded as | <H2> PPR PROGRAM </H2> | ||
Guaranteeing high quality next-generation sequencing (NGS) data in a rapidly changing environment is an ongoing challenge. The recent introduction of the [BioMicroCenter:Sequencing|Illumina NextSeq500] and the depreciation of specific metrics from Illumina's Sequencing Analysis Viewer (SAV) have made it more difficult to directly determine the baseline error rate of sequencing runs. We have created an open-source tool to construct the Percent Perfect Reads (PPR) plot previously provided by the Illumina sequencers. The PPR program is compatible with HiSeq2000/2500, MiSeq, and NextSeq500 instruments, and provides an alternative to Illumina's Q scores for determining run quality. | |||
<LI> PPR Program can be downloaded as tarball (.tgz) file [[Media:NGS_sequencing_QC.zip|'''here''']]<br> | |||
The software is designed to be run in a UNIX/LINUX environment. | |||
<H2>Dependencies:</H2> | |||
<LI>[http://hannonlab.cshl.edu/fastx_toolkit/ fastxtoolkit] (confirmed for v0.0.13) | |||
<LI>[http://bowtie-bio.sourceforge.net/bowtie2/index.shtml bowtie2] (confirmed for v2.2.3) | |||
<LI>[http://bedtools.readthedocs.io/en/latest/ bedtools] (confirmed for v2.20.1) | |||
<LI>[https://www.r-project.org/ r] (confirmed for v2.15.3) | |||
<H2>Commands:</H2> | |||
<H3>GENERIC:</H3> | |||
./NGS_missmatch_qc.pl [RUNTYPE] (FASTQ FILES) | |||
<H3>SPECIFIC:</H3> | |||
For Paired end NextSeq sequencing: | |||
./NGS_missmatch_qc.pl nextseq_paired_end read1.fq read2.fq | |||
For single end NextSeq sequencing: | |||
./NGS_missmatch_qc.pl nextseq_single_end read1.fq | |||
For paired end MiSeq sequencing: | |||
./NGS_missmatch_qc.pl miseq_paired_end read1.fq read2.fq | |||
For single end MiSeq sequencing | |||
./NGS_missmatch_qc.pl miseq_single_end read1.fq | |||
For paired end HiSeq sequencing | |||
./NGS_missmatch_qc.pl hiseq_paired_end Lane1_1.fq Lane1_2.fq Lane2_1.fq Lane2_2.fq Lane3_1.fq Lane3_2.fq Lane4_1.fq Lane4_2.fq Lane5_1.fq Lane5_2.fq Lane6_1.fq Lane6_2.fq Lane7_1.fq Lane7_2.fq Lane8_1.fq Lane8_2.fq | |||
For single end HiSeq sequencing | |||
./NGS_missmatch_qc.pl hiseq_single_end Lane1.fq Lane2.fq Lane3.fq Lane4.fq Lane5.fq Lane6.fq Lane7.fq Lane8.fq | |||
Revision as of 07:24, 17 May 2016
| HOME -- | SEQUENCING -- | LIBRARY PREP -- | HIGH-THROUGHPUT -- | COMPUTING -- | OTHER TECHNOLOGY |
PPR PROGRAM
Guaranteeing high quality next-generation sequencing (NGS) data in a rapidly changing environment is an ongoing challenge. The recent introduction of the [BioMicroCenter:Sequencing|Illumina NextSeq500] and the depreciation of specific metrics from Illumina's Sequencing Analysis Viewer (SAV) have made it more difficult to directly determine the baseline error rate of sequencing runs. We have created an open-source tool to construct the Percent Perfect Reads (PPR) plot previously provided by the Illumina sequencers. The PPR program is compatible with HiSeq2000/2500, MiSeq, and NextSeq500 instruments, and provides an alternative to Illumina's Q scores for determining run quality.
The software is designed to be run in a UNIX/LINUX environment.
Dependencies:
Commands:
GENERIC:
./NGS_missmatch_qc.pl [RUNTYPE] (FASTQ FILES)
SPECIFIC:
For Paired end NextSeq sequencing:
./NGS_missmatch_qc.pl nextseq_paired_end read1.fq read2.fq
For single end NextSeq sequencing:
./NGS_missmatch_qc.pl nextseq_single_end read1.fq
For paired end MiSeq sequencing:
./NGS_missmatch_qc.pl miseq_paired_end read1.fq read2.fq
For single end MiSeq sequencing
./NGS_missmatch_qc.pl miseq_single_end read1.fq
For paired end HiSeq sequencing
./NGS_missmatch_qc.pl hiseq_paired_end Lane1_1.fq Lane1_2.fq Lane2_1.fq Lane2_2.fq Lane3_1.fq Lane3_2.fq Lane4_1.fq Lane4_2.fq Lane5_1.fq Lane5_2.fq Lane6_1.fq Lane6_2.fq Lane7_1.fq Lane7_2.fq Lane8_1.fq Lane8_2.fq
For single end HiSeq sequencing
./NGS_missmatch_qc.pl hiseq_single_end Lane1.fq Lane2.fq Lane3.fq Lane4.fq Lane5.fq Lane6.fq Lane7.fq Lane8.fq
