[Debian-med-packaging] Bug#906332: ITP: minimap2 -- versatile pairwise aligner for genomic and spliced nucleotide sequences
Andreas Tille
tille at debian.org
Fri Aug 17 12:07:36 BST 2018
Package: wnpp
Severity: wishlist
Owner: Andreas Tille <tille at debian.org>
* Package name : minimap2
Version : 2.12
Upstream Author : Copyright: © 2017-2018 Broad Institute <hengli at broadinstitute.org>
* URL : https://github.com/lh3/minimap2
* License : MIT
Programming Lang: C
Description : versatile pairwise aligner for genomic and spliced nucleotide sequences
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 or the preprint.
Remark: This package is maintained by Debian Med Packaging Team at
https://salsa.debian.org/med-team/minimap2
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