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biology/rainbow: Efficient clustering and assembling of short reads
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Authored by jwb on Apr 1 2018, 4:08 PM.

Details

Summary

biology/rainbow: Efficient clustering and assembling of short reads

Approved by jrm (mentor) or wen (mentor)
Differential to be added to commit message

Test Plan

portlint -A: looks fine
Passed poudriere on {10.3,11.1}-{amd64,i386}
Tested in production as dependency of ddocent

Diff Detail

Repository
rP FreeBSD ports repository
Lint
Automatic diff as part of commit; lint not applicable.
Unit
Automatic diff as part of commit; unit tests not applicable.

Event Timeline

biology/rainbow/Makefile
5 ↗(On Diff #40961)

-wip

biology/rainbow/pkg-descr
1 ↗(On Diff #40961)

It is a pain when upstream only describes their program with one sentence, but I and others have been given feedback to put more than one sentence in pkg-descr. Maybe this based on the paper's abstract?

Rainbow provides an ultra-fast and memory-efficient solution to clustering and assembling short genetic sequence reads produced by Restriction site Associated DNA Sequencing (RAD-seq).  It does this by, first, clustering reads using a spaced seed method, then it divides potential groups into haplotypes in a top-down manner.  Next, along a guide tree, it iteratively merges sibling leaves in a bottom-up manner if they are similar enough.  Finally, Rainbow uses a greedy algorithm to locally assemble merged reads into contigs.  Both optimal and suboptimal assembly results are output.

wip: Just seeing if you were paying attention. ;-)

pkg-descr: Thanks for the tip and the description. Maybe marcus would be
willing to add a check to portlint. Seems like it should be pretty easy.

This revision is now accepted and ready to land.Apr 2 2018, 2:11 AM
This revision was automatically updated to reflect the committed changes.