loopy

module

v0.0.0-...-735d4ee Latest Latest Go to latest Published: Jan 15, 2020 License: BSD-3-Clause

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Repository

github.com/kortschak/loopy

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README ¶

loopy implements structural variation analysis using the Pacific Biosciences blasr aligner. It is a close run-alike to the bridgemapper tool.

Installation

loopy requires a Go installation, and a runnable blasr executable (version 5.1+).

Documentation

http://godoc.org/github.com/kortschak/loopy

License

loopy is distributed under a modified BSD license.

Directories ¶

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Path	Synopsis
blasr Package blasr provides interaction with the BLASR long read aligner.	Package blasr provides interaction with the BLASR long read aligner.
cmd
bilge bilge filters a set of sequences for low complexity.	bilge filters a set of sequences for low complexity.
broadside broadside reports the repeat types and counts for each group of events in a trio of individuals from a press GFF on stdin.	broadside reports the repeat types and counts for each group of events in a trio of individuals from a press GFF on stdin.
bundle 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.	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 carta renders a rings plot of a binned feature distribution on hg19.	carta renders a rings plot of a binned feature distribution on hg19.
catch catch looks for target site duplications flanking reefer event output by press.	catch looks for target site duplications flanking reefer event output by press.
catch-global catch-global looks for target site duplications flanking reefer event output by press-global.	catch-global looks for target site duplications flanking reefer event output by press-global.
dedup-ccs dedup-ccs breaks fasta sequences from a PB sequencing run into uniquely identified and non-uniquely identified lists.	dedup-ccs breaks fasta sequences from a PB sequencing run into uniquely identified and non-uniquely identified lists.
dedup-ccs-event 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.	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 fathom filters events based on length of element, reading from stdin.	fathom filters events based on length of element, reading from stdin.
grouper grouper reports the genomic extent of a group of reefer features where the group has been identified by press or press-global.	grouper reports the genomic extent of a group of reefer features where the group has been identified by press or press-global.
keelhaul keelhaul drops fasta sequences from stdin containing IDs in the exclude parameter file.	keelhaul drops fasta sequences from stdin containing IDs in the exclude parameter file.
loopy loopy performs blasr alignment and unmapped flank remapping to identify candidate structural variation features.	loopy performs blasr alignment and unmapped flank remapping to identify candidate structural variation features.
mangle mangle does name mangling on a multiple fasta sequence file.	mangle does name mangling on a multiple fasta sequence file.
net net performs set operation on reefer pressed events.	net performs set operation on reefer pressed events.
plank plank drops GFF lines from stdin containing Read attributes in the exclude parameter file.	plank drops GFF lines from stdin containing Read attributes in the exclude parameter file.
press press identifies, annotates and counts unique reefer events.	press identifies, annotates and counts unique reefer events.
press-global press-global identifies, annotates and counts unique reefer events without reference to a set of censor annotations.	press-global identifies, annotates and counts unique reefer events without reference to a set of censor annotations.
ranks ranks reports the repeat types and counts for each group from a GFF on stdin.	ranks reports the repeat types and counts for each group from a GFF on stdin.
reefer reefer performs blasr alignment and analysis of internal mismatches to identify candidate structural variation features.	reefer performs blasr alignment and analysis of internal mismatches to identify candidate structural variation features.
rinse 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.	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 roll outputs a list of read names from a reefer (or later) GFF outout on stdin.	roll outputs a list of read names from a reefer (or later) GFF outout on stdin.
sea-bed sea-bed outputs a set of fasta sequences based on a reference and set of bed files.	sea-bed outputs a set of fasta sequences based on a reference and set of bed files.
wring wring extracts a set of sequences from a SAM file based on a reefer GFF.	wring extracts a set of sequences from a SAM file based on a reefer GFF.