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.
Release numerous ports to ports@
I've been retired for a few years, and it is unlikely I will be doing
any more scientific computing support in the future. I have continued
to maintain ~160 ports to the best of my ability, mainly as a favor to
the community, but I can no longer justify the time and effort
required. I am therefore releasing most of my scientific ports, along
with a few others, to ports@. I will continue to maintain ports I am
actively using and those for which I am upstream.
Remove WWW entries moved into port Makefiles
Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.
This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.
Approved by: portmgr (tcberner)
Add WWW entries to port Makefiles
It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.
Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.
There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above )
biology/rainbow: Efficient clustering and assembling of short reads
Approved by: jrm (mentor)
Differential Revision: https://reviews.freebsd.org/D14924
