biology/minimap2 - The NetBSD Packages Collection

Sequence alignment program for noisy, long reads

Minimap2 is a versatile sequence alignment program that aligns DNA or
mRNA sequences against a large reference database. Typical use cases
include: (1) mapping PacBio or Oxford Nanopore genomic reads to the
human genome; (2) finding overlaps between long reads with error rate
up to ~15%; (3) splice-aware alignment of PacBio Iso-Seq or Nanopore
cDNA or Direct RNA reads against a reference genome; (4) aligning
Illumina single- or paired-end reads; (5) assembly-to-assembly
alignment; (6) full-genome alignment between two closely related
species with divergence below ~15%.

For ~10kb noisy reads sequences, minimap2 is tens of times faster than
mainstream long-read mappers such as BLASR, BWA-MEM, NGMLR and
GMAP. It is more accurate on simulated long reads and produces
biologically meaningful alignment ready for downstream analyses. For
>100bp Illumina short reads, minimap2 is three times as fast as
BWA-MEM and Bowtie2, and as accurate on simulated data.  Detailed
evaluations are available from the minimap2 paper
(https://doi.org/10.1093/bioinformatics/bty191).

Build dependencies

devel/gmake pkgtools/cwrappers

Runtime dependencies

(none)

Binary packages

OSArchitectureVersion
NetBSD 9.0i386minimap2-2.18nb1.tgz
NetBSD 9.0i386minimap2-2.18nb1.tgz
NetBSD 9.0i386minimap2-2.24.tgz
NetBSD 9.0x86_64minimap2-2.24.tgz
NetBSD 9.0x86_64minimap2-2.24.tgz
NetBSD 9.0x86_64minimap2-2.24.tgz
NetBSD 9.0x86_64minimap2-2.18nb1.tgz
NetBSD 9.0x86_64minimap2-2.18nb1.tgz
NetBSD 9.0x86_64minimap2-2.18nb1.tgz
NetBSD 9.0x86_64minimap2-2.24.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.