diff --git a/minimap2.html b/minimap2.html index 042446e..72f2c3a 100644 --- a/minimap2.html +++ b/minimap2.html @@ -61,7 +61,7 @@ p { text-align: justify; } -Manual Page - minimap2(1) +minimap2.1
@@ -172,6 +172,13 @@ Load at most NUM may be ending with k/K/m/M/g/G. NB: mapping quality is incorrect given a multi-part index. + +--idx-no-seq   +Don’t store target sequences in the index. It saves disk space and memory but +the index generated with this option will not work with +-a or +-c. When base-level alignment is not requested, this option is automatically applied. + -d FILE Save the minimizer index of @@ -344,6 +351,15 @@ accuracy by several percents, so it is applied by default with on SIRV data, please add --splice-flank=no to the command line. + +--end-seed-pen INT   +Drop a terminal anchor if +s<log(g)+INT, where +s is the local alignment score around the anchor and +g the length of the terminal gap in the chain. This option is only effective +with +--splice. It helps to avoid tiny terminal exons. [6] + @@ -563,7 +579,7 @@ the SAM-like typed key-value format. Minimap2 may output the following tags: TagTypeDescription -tpAType of aln: P/primary, S/secondary and I/inversion +tpAType of aln: P/primary, S/secondary and I,i/inversion cmiNumber of minimizers on the chain @@ -640,4 +656,4 @@ non-SSE2 support, but it would make minimap2 slower by several times. miniasm(1), minimap(1), bwa(1).

-
minimap2-2.5 (r572) minimap2 (1) 11 November 2017
+
minimap2-2.6 (r623) minimap2 (1) 12 December 2017