Fastq-join joins two paired-end reads on the overlapping ends. Basically, it assembles overlapping paired-end reads into a single contig for each pair. This increases the read length and hopefully the quality of a de novo or reference assembly. It uses squared distance for anchored alignment just like other tools in ea-utils
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.