update for minimap options

docs/options/alignment.md

@@ -288,9 +288,33 @@ For reads that have multiple alignments a random alignment is written out to a s
   Sets the reference gap open (&lt;int1>) and extend (&lt;int2>) penalties. A reference gap of length N gets a penalty of `<int1> + N * <int2>`. Default: 5, 3.
 
 
+#### MINIMAP2-SPECIFIC OPTIONS:
+
+
+- `--minimap2/--mm2`
+
+Uses minimap2 as the underlying read aligner. This mode is very new and currently experimental. Expect that things may change in the near future. The default mapping mode is `--nanopore` (preset `-x map-ont` (Nanopore reads)). Internally, minimap2 is run with the options `-a --MD`. More information here: https://lh3.github.io/minimap2/minimap2.html. Default: OFF.
+
+- `--mm2_nanopore`
+
+Using the minimap2 preset for Oxford Nanopore (ONT) vs reference mapping (`-x map-ont`). Only works in conjuntion with `--minimap2`. Default mode when `--minimap2` is specified without additional qualifiers.
+
+- `--mm2_pacbio`
+
+Using the minimap2 preset for PacBio vs reference mapping (`-x map-pb`). Only works in conjuntion with `--minimap2`. Default: OFF.
+
+- `--mm2_short_reads`
+
+This option invokes the minmap2 preset setting `-x sr` and is intended for genomic short-read mapping with accurate reads (probably Illumina 150bp+ ?). For spliced short-reads, please use `--hisat2` instead. The `sr` preset mode (short single-end reads without splicing) uses the following options:
+`-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`. Default: OFF.
+
+- `--mm2_maximum_length <int>`
+
+Maximum length cutoff for very long sequences (currently allowed 100-100,000 bp). Default: 10000.
+
 #### OUTPUT:
 
-The output is a BAM format by default, as well as a aligment report deduplication report (ending in '_deduplication_report.txt')
+The output is a BAM file by default, as well as a aligment report text file.
 
 For a single-end file called 'simulated.fastq', the expected output for Bowtie 2, HISAT2 or minimap2 is:
 
@@ -303,7 +327,7 @@ simulated_bismark_mm2.bam
 simulated_bismark_mm2_SE_report.txt
 ```
 
-In a paired-end situation, for files 'simulated_1.fastq' and 'simulated_2.fastq' you would expect for Bowtie2 or HISAT2:
+In a paired-end situation, for files 'simulated_1.fastq' and 'simulated_2.fastq' you would expect the following result files Bowtie2 or HISAT2:
 
 ```
 simulated_1_bismark_bt2_pe.bam