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Release minimap2-2.0 (r275)

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Heng Li 2017-08-08 21:16:25 -04:00
parent 8c2917b391
commit 6840370f3c
3 changed files with 42 additions and 15 deletions
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13
NEWS.md
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Release 2.0-r275 (8 August 2017)
--------------------------------
This release is identical to version 2.0rc1, except the version number. It is
described and evaluated in the following technical report:
* Li, H. (2017). Minimap2: fast pairwise alignment for long DNA sequences.
[arXiv:1708.01492v1](https://arxiv.org/abs/1708.01492v1).
(2.0: 8 August 2017, r275)
Release 2.0rc1-r232 (30 July 2017)
----------------------------------

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main.c
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#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0rc1-r232"
#define MM_VERSION "2.0-r275"
void liftrlimit()
{

42
minimap2.1
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.TH minimap2 1 "30 July 2017" "minimap2-2.0rc1-r232" "Bioinformatics tools"
.TH minimap2 1 "8 August 2017" "minimap2-2.0-r275" "Bioinformatics tools"
.SH NAME
.PP
minimap2 - mapping and alignment between collections of DNA sequences
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.RS
.TP 8
.B map-pb
PacBio/Oxford Nanopore read to reference mapping (-Hk19)
PacBio/Oxford Nanopore read to reference mapping
.RB ( -Hk19 )
.TP
.B map10k
The same as
.B map-pb
(-Hk19)
.RB ( -Hk19 )
.TP
.B map-ont
Slightly more sensitive for Oxford Nanopore to reference mapping (-k15). For
PacBio reads, HPC minimizers consistently leads to faster performance and more
sensitive results in comparison to normal minimizers. For Oxford Nanopore data,
normal minimizers are better, though not much. The effectiveness of HPC is
determined by the sequencing error mode.
Slightly more sensitive for Oxford Nanopore to reference mapping
.RB ( -k15 ).
For PacBio reads, HPC minimizers consistently leads to faster performance and
more sensitive results in comparison to normal minimizers. For Oxford Nanopore
data, normal minimizers are better, though not much. The effectiveness of HPC
is determined by the sequencing error mode.
.TP
.B asm5
Long assembly to reference mapping (-k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200).
Long assembly to reference mapping
.RB ( -k19
.B -w19 -A1 -B19 -O39,81 -E3,1 -s200
.BR -z200 ).
Typically, the alignment will not extend to regions with 5% or higher sequence
divergence. Only use this preset if the average divergence is far below 5%.
.TP
.B asm10
Long assembly to reference mapping (-k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200). Up
to 10% sequence divergence.
Long assembly to reference mapping
.RB ( -k19
.B -w19 -A1 -B9 -O16,41 -E2,1 -s200
.BR -z200 ).
Up to 10% sequence divergence.
.TP 8
.B ava-pb
PacBio all-vs-all overlap mapping (-Hk19 -w5 -Xp0 -m100 -K500m -g10000 --max-chain-skip 25)
PacBio all-vs-all overlap mapping
.RB ( -Hk19
.B -w5 -Xp0 -m100 -K500m -g10000 --max-chain-skip
.BR 25 ).
.TP 8
.B ava-ont
Oxford Nanopore all-vs-all overlap mapping (-k15 -w5 -Xp0 -m100 -K500m -g10000
--max-chain-skip 25). Similarly, the major difference from
Oxford Nanopore all-vs-all overlap mapping
.RB ( -k15
.B -w5 -Xp0 -m100 -K500m -g10000 --max-chain-skip
.BR 25 ).
Similarly, the major difference from
.B ava-pb
is that this preset is not using HPC minimizers.
.RE