Input
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
*.{fq,fastq,fq.gz,fastq.gz}
Output
Adapter trimmed FastQ files of either single-end reads, or singleton
‘orphaned’ reads from merging of paired-end data (i.e., one of the pair
was lost due to filtering thresholds).
*.truncated.fastq.gz
Adapter trimmed FastQ files of reads that did not pass filtering
thresholds.
*.discarded.fastq.gz
Adapter trimmed R1 FastQ files of paired-end reads that did not merge
with their respective R2 pair due to long templates. The respective pair
is stored in ‘pair2_truncated’.
*.pair1.truncated.fastq.gz
Adapter trimmed R2 FastQ files of paired-end reads that did not merge
with their respective R1 pair due to long templates. The respective pair
is stored in ‘pair1_truncated’.
*.pair2.truncated.fastq.gz
Collapsed FastQ of paired-end reads that successfully merged with their
respective R1 pair but were not trimmed.
*.collapsed.fastq.gz
Collapsed FastQ of paired-end reads that successfully merged with their
respective R1 pair and were trimmed of adapter due to sufficient overlap.
*.collapsed.truncated.fastq.gz
