Bug#995422: ITP: long-read-assembler -- assembly from long reads against reference genome
Package: wnpp
Severity: wishlist
Subject: ITP: long-read-assembler -- assembly from long reads against reference genome
Package: wnpp
Owner: Steffen Moeller <moeller@debian.org>
Severity: wishlist
* Package name : long-read-assembler
Version : 1.3.2
Upstream Author : Copyright: Bonnie Phan Wolfe <bonniep@usc.edu>
* URL : https://github.com/ChaissonLab/LRA
* License : USC-RL-1.0
Programming Lang: C
Description : assembly from long reads against reference genome
Machines that determine the DNA sequence do not provide answers
en block, but as many comparatively short reads that by chance
also overlap. From these, the complete genome is puzzled together
assembled. This is less easy than one may think because of
redundancies of the genome, so you do not know where a read comes
from if that read is too short. A reference genome helps, but
people differ, e.g. with local duplications, and you may be
interested in diseases that have chromosomal rearrangements.
.
lra is a sequence alignment program that aligns long reads from
single-molecule sequencing (SMS) instruments, or megabase-scale contigs
from SMS assemblies. These technologies provide reads that are 1000 or
10k times longer than what can be achieved with the Sanger Sequencing
technology and help the assembly.
.
lra implements seed chaining sparse dynamic programming with a concave
gap function to read and assembly alignment, which is also extended to
allow for inversion cases. lra alignment approach increases sensitivity
and specificity for SV discovery, particularly for variants above 1kb
and when discovering variation from ONT reads, while having runtime
that arecomparable (1.05-3.76×) to current methods. When applied to
calling variation from *de novo* assembly contigs, there is a 3.2%
increase in Truvari F1 score compared to minimap2+htsbox.
Remark: This package is maintained by Steffen Moeller at
https://salsa.debian.org/med-team/long-read-assembler
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