From 81b3da7677359e9bbd33b8539442f54efa6e7e9f Mon Sep 17 00:00:00 2001 From: Heng Li Date: Sat, 26 Jun 2021 19:29:14 -0400 Subject: [PATCH] updated the manpage --- minimap2.html | 106 ++++++++++++++++++++++++++------------------------ 1 file changed, 56 insertions(+), 50 deletions(-) diff --git a/minimap2.html b/minimap2.html index e521044..a30e08f 100644 --- a/minimap2.html +++ b/minimap2.html @@ -216,20 +216,27 @@ ignore minimizers occuring more than -xsr mode, which sets the threshold for a second round of seeding. ---min-occ-floor INT   -Force minimap2 to always use k-mers occurring -INT times or less [0]. In effect, the max occurrence threshold is set to -the -max{INT, -f}. - --g INT -Stop chain enlongation if there are no minimizers within -INT-bp [10000]. +-U INT1[,INT2]   +Lower and upper bounds of k-mer occurrences [10,1000000]. The final k-mer occurrence threshold is +max{INT1, min{INT2, -f}}. This option prevents excessively small or large +-f estimated from the input reference. It deprecates +--min-occ-floor in earlier versions of minimap2. --r INT -Bandwidth used in chaining and DP-based alignment [500]. This option -approximately controls the maximum gap size. +-e INT +Sample a high-frequency minimizer every +INT basepairs [500]. + + +-g NUM +Stop chain enlongation if there are no minimizers within +NUM-bp [10k]. + + +-r NUM1[,NUM2]   +Bandwidth for chaining and base alignment [500,20k]. +NUM1 is used for initial chaining and alignment extension; +NUM2 for RMQ-based re-chaining and closing gaps in alignments. -n INT @@ -298,6 +305,11 @@ Mark as secondary a chain that overlaps with a better chain by FLOAT or more of the shorter chain [0.5] +--rmq=no|yes   +Use the minigraph chaining algorithm [no]. The minigraph algorithm is better +for aligning contigs through long INDELs. + + --hard-mask-level   Honor option -M and disable a heurstic to save unmapped subsequences and disables @@ -330,11 +342,6 @@ Scale of gap cost during chaining [1.0] Disable the long gap patching heuristic. When this option is applied, the maximum alignment gap is mostly controlled by -r. - ---lj-min-ratio FLOAT   -Fraction of query sequence length required to bridge a long gap [0.5]. A -smaller value helps to recover longer gaps, at the cost of more false gaps. - --splice Enable the splice alignment mode. @@ -483,7 +490,7 @@ alignment. --cap-sw-mem NUM   Skip alignment if the DP matrix size is above -NUM. Set 0 to disable [0]. +NUM. Set 0 to disable [100m]. @@ -614,61 +621,60 @@ values set by - - - + + - - - - - - - + +
-map-pb -PacBio/Oxford Nanopore read to reference mapping -(-Hk19)
+
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. +Align noisy long reads of ~10% error rate to a reference genome. This is the +default mode.
+
+map-hifi +Align PacBio high-fidelity (HiFi) reads to a reference genome +(-k19 -w19 -U50,500 -g10k -A1 -B4 -O6,26 -E2,1 -s200).
+map-pb +Align older PacBio continuous long (CLR) reads to a reference genome +(-Hk19).
asm5 Long assembly to reference mapping -(-k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 -N50 --min-occ-floor=100). Typically, the alignment will not extend to regions with 5% or higher sequence +(-k19 -w19 -U50,500 --rmq -r100k -g10k -A1 -B19 -O39,81 -E3,1 -s200 -z200 -N50). 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%.
+
asm10 Long assembly to reference mapping -(-k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 -N50 --min-occ-floor=100). Up to 10% sequence divergence. +(-k19 -w19 -U50,500 --rmq -r100k -g10k -A1 -B9 -O16,41 -E2,1 -s200 -z200 -N50). Up to 10% sequence divergence.
+
asm20 Long assembly to reference mapping -(-k19 -w10 -A1 -B4 -O6,26 -E2,1 -s200 -z200 -N50 --min-occ-floor=100). Up to 20% sequence divergence. +(-k19 -w10 -U50,500 --rmq -r100k -g10k -A1 -B4 -O6,26 -E2,1 -s200 -z200 -N50). Up to 20% sequence divergence.
-ava-pb -PacBio all-vs-all overlap mapping -(-Hk19 -Xw5 -m100 -g10000 --max-chain-skip 25).
-ava-ont -Oxford Nanopore all-vs-all overlap mapping -(-k15 -Xw5 -m100 -g10000 -r2000 --max-chain-skip 25). Similarly, the major difference from -ava-pb is that this preset is not using HPC minimizers. -
+
splice Long-read spliced alignment -(-k15 -w5 --splice -g2000 -G200k -A1 -B2 -O2,32 -E1,0 -C9 -z200 -ub --junc-bonus=9 --splice-flank=yes). In the splice mode, 1) long deletions are taken as introns and represented as +(-k15 -w5 --splice -g2k -G200k -A1 -B2 -O2,32 -E1,0 -C9 -z200 -ub --junc-bonus=9 --cap-sw-mem=0 --splice-flank=yes). In the splice mode, 1) long deletions are taken as introns and represented as the ‘N’ CIGAR operator; 2) long insertions are disabled; 3) deletion and insertion gap costs are different during chaining; 4) the computation of the ‘ms’ tag ignores introns to demote hits to pseudogenes.
-splice:hq
  +
+splice:hq Long-read splice alignment for PacBio CCS reads (-xsplice -C5 -O6,24 -B4).
+
sr Short single-end reads without splicing (-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).
+ava-pb +PacBio CLR all-vs-all overlap mapping +(-Hk19 -Xw5 -e0 -m100).
+ava-ont +Oxford Nanopore all-vs-all overlap mapping +(-k15 -Xw5 -e0 -m100 -r2k).
@@ -831,4 +837,4 @@ non-SSE2/NEON support, but it would make minimap2 slower by several times. miniasm(1), minimap(1), bwa(1).

-
minimap2-2.18 (r1015) minimap2 (1) 9 April 2021
+
minimap2-2.20 (r1061) minimap2 (1) 27 May 2021