Fastq-stats calculates basic statistics for fastq files including counting of duplicates. It can produces following information about fastq files: number of reads in the fastq file; read length (mean and stdev); phred scale used; number of reads used to generate duplicate read statistics; number of bases to assess for duplicity; number of reads that are duplicates; number sequences that are duplicated; base Quality min, max and mean; base percentages and total number of bases
Parent program: ea-utils
Ea-utils is FASTQ processing utilities such as fastq-mcf, fastq-multx, fastq-join, varcall and sam-stats and other. These tools detect and remove sequencing adapters and primers, detect limited skewing at the ends of reads and clip, poor quality at the ends of reads and clip, discard sequences that are too short after all of the above, keep multiple mate-reads in sync while doing all of the above, merge overlapping paired-end reads and computing statisticsfrom SAM, BAM or Fasta files.