diff --git a/minimap2.html b/minimap2.html index 11c2e1e..75b082c 100644 --- a/minimap2.html +++ b/minimap2.html @@ -196,11 +196,22 @@ provided as the target sequences, options
- + - + @@ -441,6 +463,10 @@ Output the short is assumed. [none] + @@ -511,13 +537,18 @@ is determined by the sequencing error mode. + + + @@ -694,4 +727,4 @@ non-SSE2/NEON support, but it would make minimap2 slower by several times. miniasm(1), minimap(1), bwa(1).

-
--f FLOAT -Ignore top -FLOAT fraction of most frequent minimizers [0.0002] +
+-f FLOAT|INT1[,INT2]
  +If fraction, ignore top +FLOAT fraction of most frequent minimizers [0.0002]. If integer, +ignore minimizers occuring more than +INT1 times. +INT2 is only effective in the +--sr or +-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 @@ -351,12 +362,19 @@ min{O1+k*E1,O2+k*E2}. In the splice mo Cost for a non-canonical GT-AG splicing (effective with --splice) [0]
--z INT -Break an alignment if the running score drops too quickly along the diagonal of -the DP matrix (diagonal X-drop, or Z-drop) [400]. Increasing the value improves -the contiguity of the alignment at the cost of poor alignment in the middle -(e.g. caused by a long inversion). +
+-z INT1[,INT2]
  +Truncate an alignment if the running alignment score drops too quickly along +the diagonal of the DP matrix (diagonal X-drop, or Z-drop) [400,200]. If the +drop of score is above +INT2, minimap2 will reverse complement the query in the related region and align +again to test small inversions. Minimap2 truncates alignment if there is an +inversion or the drop of score is greater than +INT1. Decrease +INT2 to find small inversions at the cost of performance and false positives. +Increase +INT1 to improves the contiguity of alignment at the cost of poor alignment in the +middle.
-s INT @@ -427,6 +445,10 @@ SAM read group line in a format like @RG\\tID:foo\\tSM:bar [].
+-y +Copy input FASTA/Q comments to output. +
-c Generate CIGAR. In PAF, the CIGAR is written to the ‘cg’ custom tag.
+--MD +Output the MD tag (see the SAM spec). +
-Y In SAM output, use soft clipping for supplementary alignments.
asm5 Long assembly to reference mapping -(-k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200). Typically, the alignment will not extend to regions with 5% or higher sequence +(-k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 --min-occ-floor=100). 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). Up to 10% sequence divergence. +(-k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 --min-occ-floor=100). Up to 10% sequence divergence. +
+asm20 +Long assembly to reference mapping +(-k19 -w10 -A1 -B6 -O6,26 -E2,1 -s200 -z200 --min-occ-floor=100). Up to 20% sequence divergence.
ava-pb @@ -526,7 +557,7 @@ PacBio all-vs-all overlap mapping
ava-ont Oxford Nanopore all-vs-all overlap mapping -(-k15 -Xw5 -m100 -g10000 --max-chain-skip 25). Similarly, the major difference from +(-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.
@@ -627,6 +658,8 @@ the SAM-like typed key-value format. Minimap2 may output the following tags:
NMiTotal number of mismatches and gaps in the alignment
MDZTo generate the ref sequence in the alignment
ASiDP alignment score
msiDP score of the max scoring segment in the alignment
minimap2-2.8 (r672) minimap2 (1) 1 February 2018
+
minimap2-2.10 (r761) minimap2 (1) 27 March 2018