biology/rainbow: Efficient clustering and assembling of short reads
Approved by jrm (mentor) or wen (mentor)
Differential to be added to commit message
Details
Details
portlint -A: looks fine
Passed poudriere on {10.3,11.1}-{amd64,i386}
Tested in production as dependency of ddocent
Diff Detail
Diff Detail
- Repository
- rP FreeBSD ports repository
- Lint
No Lint Coverage - Unit
No Test Coverage - Build Status
Buildable 15915 Build 15907: arc lint + arc unit
Event Timeline
| biology/rainbow/Makefile | ||
|---|---|---|
| 5 | -wip | |
| biology/rainbow/pkg-descr | ||
| 1 | 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. | |
Comment Actions
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.