LFPE: SOP 1063
Updated: 2016-10-24
RQC Read Filtering Methods


Sequence data for library <library_name> was generated at the DOE Joint Genome Institute (JGI) using Illumina technology [1].  An Illumina <library type> was constructed and sequenced <sequencing_run_mode> using the Illumina <sequencer_name> platform which generated <raw_read_count> reads totaling <raw_base_count> bp.  BBDuk (version <bbtools version>) [2] was used to remove contaminants [3],  trim reads that contained DNA specific sequencing artifacts, right quality trim reads where quality drops below 6 and right trim reads where the LFPE linker was found.  BBDuk was used to remove reads that contained 1 or more 'N' bases, had an average quality score across the read less than 10 or had a minimum length <= 51 bp or 33% of the full read length.  Reads mapped with BBMap [2] to masked [5] human, cat, dog and mouse references at 93% identity were separated into a chaff file [4].  Reads aligned to common microbial contaminants [6] were separated into a chaff file [4].  The final filtered fastq contained <filtered_read_count> reads totalling <filtered_base_count> bp.


1. SOP 1063
2. B. Bushnell: BBTools software package, http:\\bbtools.jgi.doe.gov
3. BBDuk, BBMap and BBMerge commands used for filtering are placed in file:
<filter_command_file>
4. All removed reads are placed in file:
<filter_chaff_fastq_file>
5. Filtering references file:
filtering_references-20160921.tar
6. SOP 1077


