This mode is used to concatenate compact reads files, count the number of reads, and track the min and max sequence length of all of the reads It is implemented by edu.cornell.med.icb.goby.modes.ConcatenateCompactReadsMode.java.

Mode Parameters

The following options are available in this mode

FlagArgumentsRequiredDescription
(-o|--output)outputnoThe output filename.
n/ainputyesThe basenames of the input alignments to concatenate.
(-n|--sequence-per-chunk)sequence-per-chunknoThe number of sequences that will be written in each compressed chunk. Default is suitable for very many short sequences. Reduce to a few sequences per chunk if each sequence is very large.