cmd/

bilge filters a set of sequences for low complexity.

broadside reports the repeat types and counts for each group of events in a trio of individuals from a press GFF on stdin.

bundle splits a multiple fasta sequence file into a number of multiple fasta sequence files that are no greater in sequence length than a defined theshold.

carta renders a rings plot of a binned feature distribution on hg19.

catch looks for target site duplications flanking reefer event output by press.

catch-global looks for target site duplications flanking reefer event output by press-global.

dedup-ccs breaks fasta sequences from a PB sequencing run into uniquely identified and non-uniquely identified lists.

dedup-ccs-event breaks gff features from a PB sequencing run and blasr alignment passed through the reefer pipeline into uniquely identified and non-uniquely identified lists.

fathom filters events based on length of element, reading from stdin.

grouper reports the genomic extent of a group of reefer features where the group has been identified by press or press-global.

keelhaul drops fasta sequences from stdin containing IDs in the exclude parameter file.

loopy performs blasr alignment and unmapped flank remapping to identify candidate structural variation features.

mangle does name mangling on a multiple fasta sequence file.

net performs set operation on reefer pressed events.

plank drops GFF lines from stdin containing Read attributes in the exclude parameter file.

press identifies, annotates and counts unique reefer events.

press-global identifies, annotates and counts unique reefer events without reference to a set of censor annotations.

ranks reports the repeat types and counts for each group from a GFF on stdin.

reefer performs blasr alignment and analysis of internal mismatches to identify candidate structural variation features.

rinse removes events that are either too close to the end of a read or a contig, or map to a site of a repeat of the same class.

roll outputs a list of read names from a reefer (or later) GFF outout on stdin.

sea-bed outputs a set of fasta sequences based on a reference and set of bed files.

wring extracts a set of sequences from a SAM file based on a reefer GFF.