Nanopore · Python

NanoFilt using albacore sequencing_summary for quality filtering

Due to a discrepancy between the quality scores calculated from the reads and those from the sequencing_summary.txt from albacore I added an option to NanoFilt to filter using the qualities specified in the sequencing_summary.

NanoFilt now (v1.1.0) also optionally takes a --summary flag for the sequencing_summary file. As a nice bonus, it’s also faster! This added a new dependency to NanoFilt, my nanoget module which performs extraction of metrics from fastq files, bam files and sequencing_summary files and returns all information in a convenient pandas DataFrame. For fast lookup of the quality scores this DataFrame is converted to a dictionary linking the read identifier with the quality score.

 

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