biology/miniasm - The NetBSD Packages Collection

OLC-based de novo assembler for long reads

Miniasm is a very fast OLC-based *de novo* assembler for noisy long
reads. It takes all-vs-all read self-mappings (typically by minimap)
as input and outputs an assembly graph in the GFA format. Different
from mainstream assemblers, miniasm does not have a consensus step. It
simply concatenates pieces of read sequences to generate the final
unitig sequences. Thus the per-base error rate is similar to the raw
input reads.

So far miniasm is in early development stage. It has only been tested
on a dozen of PacBio and Oxford Nanopore (ONT) bacterial data
sets. Including the mapping step, it takes about 3 minutes to assemble
a bacterial genome. Under the default setting, miniasm assembles 9 out
of 12 PacBio datasets and 3 out of 4 ONT datasets into a single
contig.

Miniasm confirms that at least for high-coverage bacterial genomes, it
is possible to generate long contigs from raw PacBio or ONT reads
without error correction. It also shows that minimap can be used as a
read overlapper, even though it is probably not as sensitive as the
more sophisticated overlapers such as MHAP and DALIGNER.  Coupled with
long-read error correctors and consensus tools, miniasm may also be
useful to produce high-quality assemblies.

Build dependencies

devel/gmake pkgtools/cwrappers

Runtime dependencies

(none)

Binary packages

OSArchitectureVersion
NetBSD 9.0aarch64miniasm-0.3.tgz
NetBSD 9.0aarch64miniasm-0.3.tgz
NetBSD 9.0aarch64miniasm-0.3.tgz
NetBSD 9.0alphaminiasm-0.3.tgz
NetBSD 9.0alphaminiasm-0.3.tgz
NetBSD 9.0alphaminiasm-0.3.tgz
NetBSD 9.0sparc64miniasm-0.3.tgz
NetBSD 9.0sparc64miniasm-0.3.tgz
NetBSD 9.0sparc64miniasm-0.3.tgz
NetBSD 9.0x86_64miniasm-0.3.tgz
NetBSD 9.0x86_64miniasm-0.3.tgz
NetBSD 9.0x86_64miniasm-0.3.tgz
NetBSD 9.0x86_64miniasm-0.3.tgz
NetBSD 9.0x86_64miniasm-0.3.tgz
NetBSD 9.0x86_64miniasm-0.3.tgz
NetBSD 9.0x86_64miniasm-0.3.tgz

Binary packages can be installed with the high-level tool pkgin (which can be installed with pkg_add) or pkg_add(1) (installed by default). The NetBSD packages collection is also designed to permit easy installation from source.

Available build options

(none)

Known vulnerabilities

The pkg_admin audit command locates any installed package which has been mentioned in security advisories as having vulnerabilities.

Please note the vulnerabilities database might not be fully accurate, and not every bug is exploitable with every configuration.


Problem reports, updates or suggestions for this package should be reported with send-pr.