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## Description Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies. Racon can be used as a polishing tool after the assembly with **either Illumina data or data produced by third generation of sequencing**. The type of data inputed is automatically detected. Racon takes as input only three files: contigs in FASTA/FASTQ format, reads in FASTA/FASTQ format and overlaps/alignments between the reads and the contigs in MHAP/PAF/SAM format. Output is a set of polished contigs in FASTA format printed to stdout. All input files **can be compressed with gzip** (which will have impact on parsing time). Racon can also be used as a read error-correction tool. In this scenario, the MHAP/PAF/SAM file needs to contain pairwise overlaps between reads **including dual overlaps**. A **wrapper script** is also available to enable easier usage to the end-user for large datasets. It has the same interface as racon but adds two additional features from the outside. Sequences can be **subsampled** to decrease the total execution time (accuracy might be lower) while target sequences can be **split** into smaller chunks and run sequentially to decrease memory consumption. Both features can be run at the same time as well. |
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pkgsrc
pkgsrc is a framework for building software for a variety of UNIX-like systems.
It produces binary packages, which can be managed with tools such as
pkgin. pkgsrc is highly configurable, supporting
building packages for an arbitrary installation prefix (the default is
/usr/pkg), allowing multiple branches to coexist on one machine, a
build options framework, and a compiler transformation framework, among
other advanced features. Unprivileged use and installation is also supported.
pkgsrc is the default package manager for NetBSD and SmartOS. It's also supported as a first-class option in OmniOS CE and Oasis Linux.
Bootstrapping
To use pkgsrc on operating systems other than NetBSD, you first need to bootstrap:
cd pkgsrc/bootstrap
./bootstrap
Note that this is only for the most simple case, using pkgsrc's defaults.
Please consult bootstrap/README and bootstrap/README.OS for detailed
information about bootstrapping.
Building packages
cd pkgsrc/category/package-name
$PREFIX/bin/bmake install
Where $PREFIX is where you've chosen to install packages
(typically /usr/pkg)
On NetBSD, bmake is simply the built-in make tool.
To build packages in bulk, tools such as pkgtools/pbulk and
pkgtools/pkg_comp can be used.
Troubleshooting
- Join the community IRC channel #pkgsrc @ freenode.
- Subscribe to the pkgsrc-users mailing list
- Send bugs and patches via web form (use the
pkgcategory).
Latest sources
To fetch the main CVS repository:
cvs -d anoncvs@anoncvs.NetBSD.org:/cvsroot checkout -P pkgsrc
To work in the Git mirror, which is updated every few hours from CVS:
git clone https://github.com/NetBSD/pkgsrc.git
Additional links
- pkgsrc guide - the authoritative document on pkgsrc, also available as
doc/pkgsrc.txt - pkgsrc in the NetBSD Wiki - miscellaneous articles and tutorials
- pkgsrc.se - a searchable web index of pkgsrc
- pkgsrc-wip - a project to get more people actively involved with creating packages for pkgsrc
- pkgsrc on Twitter - announcements to the world
- pkgsrcCon - we get together
- BulkTracker - a web application that tracks pkgsrc bulk builds