From c040b0c70e1b5d9870ad1a6a8b2fac8901fa1d2e Mon Sep 17 00:00:00 2001 From: Felix Krueger Date: Fri, 16 Feb 2024 11:45:36 +0000 Subject: [PATCH] update for minimap options --- docs/options/alignment.md | 28 ++++++++++++++++++++++++++-- 1 file changed, 26 insertions(+), 2 deletions(-) diff --git a/docs/options/alignment.md b/docs/options/alignment.md index 5a424ec..90759be 100644 --- a/docs/options/alignment.md +++ b/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 (<int1>) and extend (<int2>) penalties. A reference gap of length N gets a penalty of ` + N * `. 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 ` + +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