A tool to count basepair in fastq file

• readfq

  1 19 0.0 C

  A simple tool to calculate reads number and total base count in FASTQ file (by billzt)

You can try readfq, or manually multiply total reads x average read length, those values are stored in fastqc_data.txt in *.zip archive from FastQC output.

• fastp

  9 1,775 4.7 C++

  An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

  

If you also need some other basic statistics or want to filter the reads you can try fastp (https://github.com/OpenGene/fastp). If only the basepair count is needed, awk might be the fastest solution as suggested before.

• InfluxDB

  www.influxdata.com featured

  Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.

  

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