diff --git a/minimap2.html b/minimap2.html
index 72f2c3a..1850ec2 100644
--- a/minimap2.html
+++ b/minimap2.html
@@ -203,7 +203,7 @@ Ignore top
|
-g INT |
-Stop chain enlongation if there are no minimizers in
+Stop chain enlongation if there are no minimizers within
INT-bp [10000].
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@@ -223,11 +223,26 @@ Discard chains with chaining score
concave gap penalty. It is computed with dynamic programming.
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+-D |
+If query sequence name/length are identical to the target name/length, ignore
+diagonal anchors. This option also reduces DP-based extension along the
+diagonal.
+ |
+|
+-P |
+Retain all chains and don’t attempt to set primary chains. Options
+-p and
+-N have no effect when this option is in use.
+ |
+|
+--dual=yes|no |
| |
+During chaining, whether to skip pairs wherein the query name is
+lexicographically greater than the target name [yes]
+ |
+|
-X |
-Perform all-vs-all mapping. In this mode, if the query sequence name is
-lexicographically larger than the target sequence name, the hits between them
-will be suppressed; if the query sequence name is the same as the target name,
-diagonal minimizer hits will also be suppressed.
+Equivalent to
+’-DP --dual=no --no-long-join’. Primarily used for all-vs-all read overlapping.
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|
-p FLOAT |
@@ -236,6 +251,8 @@ Between two chains overlaping over half of the shorter chain (controlled by
--mask-level), the chain with a lower score is secondary to the chain with a higher score.
If the ratio of the scores is below
FLOAT, the secondary chain will not be outputted or extended with DP alignment later.
+This option has no effect when
+-X is applied.
|
|
-N INT |
@@ -252,7 +269,12 @@ Maximum gap on the reference (effective with
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-F NUM |
Maximum fragment length (aka insert size; effective with
--xsr/--frag) [800]
+-xsr/--frag=yes) [800]
+ |
+|
+-M FLOAT |
+Mark as secondary a chain that overlaps with a better chain by
+FLOAT or more of the shorter chain [0.5]
|
|
--max-chain-skip INT |
| |
@@ -279,9 +301,24 @@ if no good chain is found. In addition, minimap2 attempts to patch gaps between
seeds with ungapped alignment.
|
|
---frag[=no|yes] |
| |
+--frag=no|yes |
| |
Whether to enable the fragment mode [no]
|
+|
+--for-only |
+Only map to the forward strand of the reference sequences. For paired-end
+reads in the forward-reverse orientation, the first read is mapped to forward
+strand of the reference and the second read to the reverse stand.
+ |
+|
+--rev-only |
+Only map to the reverse complement strand of the reference sequences.
+ |
+|
+--heap-sort=no|yes |
| |
+If yes, sort anchors with heap merge, instead of radix sort. Heap merge is
+faster for short reads, but slower for long reads. [no]
+ |
|
@@ -338,12 +375,12 @@ How to find canonical splicing sites GT-AG -
Score bonus when alignment extends to the end of the query sequence [0].
|
---splice-flank[=yes|no] |
| |
+--splice-flank=yes|no |
| |
Assume the next base to a
GT donor site tends to be A/G (91% in human and 92% in mouse) and the preceding
base to a
-AG acceptor tends to be C/T [yes with
---splice]. This trend is evolutionarily conservative, all the way to S. cerevisiae
+AG acceptor tends to be C/T [no].
+This trend is evolutionarily conservative, all the way to S. cerevisiae
(PMID:18688272). Specifying this option generally leads to higher junction
accuracy by several percents, so it is applied by default with
--splice. However, the SIRV control does not honor this trend
@@ -434,7 +471,7 @@ Similar to option
memory.
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---secondary[=yes|no] |
| |
+--secondary=yes|no |
| |
Whether to output secondary alignments [yes]
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@@ -484,11 +521,11 @@ Long assembly to reference mapping
|
|
ava-pb |
PacBio all-vs-all overlap mapping
-(-Hk19 -w5 -Xp0 -m100 -g10000 --max-chain-skip 25). |
+(-Hk19 -Xw5 -m100 -g10000 --max-chain-skip 25).
|
ava-ont |
Oxford Nanopore all-vs-all overlap mapping
-(-k15 -w5 -Xp0 -m100 -g10000 --max-chain-skip 25). Similarly, the major difference from
+(-k15 -Xw5 -m100 -g10000 --max-chain-skip 25). Similarly, the major difference from
ava-pb is that this preset is not using HPC minimizers.
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@@ -503,7 +540,7 @@ costs are different during chaining; 4) the computation of the
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sr |
Short single-end reads without splicing
-(-k21 -w11 --sr --frag -A2 -B8 -O12,32 -E2,1 -r50 -p.5 -N20 -f1000,5000 -n2 -m20 -s40 -g200 -2K50m --secondary=no). |
+(-k21 -w11 --sr --frag=yes -A2 -B8 -O12,32 -E2,1 -r50 -p.5 -N20 -f1000,5000 -n2 -m20 -s40 -g200 -2K50m --heap-sort=yes --secondary=no).
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@@ -642,8 +679,8 @@ because even the optimal alignment may be wrong in such regions.
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*
|
-Minimap2 requires SSE2 instructions to compile. It is possible to add
-non-SSE2 support, but it would make minimap2 slower by several times.
+Minimap2 requires SSE2 or NEON instructions to compile. It is possible to add
+non-SSE2/NEON support, but it would make minimap2 slower by several times.
|
|
@@ -656,4 +693,4 @@ non-SSE2 support, but it would make minimap2 slower by several times.
miniasm(1), minimap(1), bwa(1).
- | minimap2-2.6 (r623) | minimap2 (1) | 12 December 2017 |