+ new cmdline options

PombertLab · May 16, 2024 · 845ecc4 · 845ecc4
1 parent b3826a2
commit 845ecc4
Showing 1 changed file with 9 additions and 0 deletions.
diff --git a/Examples/commands.conf b/Examples/commands.conf
@@ -26,9 +26,18 @@
 ### Minimum contig size (in bp) [Default: 1]; i.e. investigates all contigs
 --minsize 1
 
+### Exclude contigs with names matching the regular expression(s); e.g. --exclude 
+# --exclude '^AUX'
+
+### Specify genome alignment tool: minimap or mashmap [Default: minimap]
+--aligner minimap
+
 ### Specify minimap2 max divergence preset (--asm 5, 10 or 20) [Default: off]
 # --asm 20
 
+### Specify mashmap percentage identity [Default: 85]
+--mpid 85
+
 ### Resume minimap2 computations (skip completed alignments)
 # --resume