From 924fc4d6712f92d53344597022e2af3eebbb195b Mon Sep 17 00:00:00 2001 From: Heng Li Date: Wed, 2 Apr 2025 13:06:03 -0400 Subject: [PATCH] minor --- README.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 34c674f..4d39499 100644 --- a/README.md +++ b/README.md @@ -14,13 +14,13 @@ cd minimap2 && make # use presets (no test data) ./minimap2 -ax map-pb ref.fa pacbio.fq.gz > aln.sam # PacBio CLR genomic reads ./minimap2 -ax map-ont ref.fa ont.fq.gz > aln.sam # Oxford Nanopore genomic reads -./minimap2 -ax map-hifi ref.fa pacbio-ccs.fq.gz > aln.sam # PacBio HiFi/CCS genomic reads (v2.19 or later) -./minimap2 -ax lr:hq ref.fa ont-Q20.fq.gz > aln.sam # Nanopore Q20 genomic reads (v2.27 or later) +./minimap2 -ax map-hifi ref.fa pacbio-ccs.fq.gz > aln.sam # PacBio HiFi/CCS genomic reads (v2.19+) +./minimap2 -ax lr:hq ref.fa ont-Q20.fq.gz > aln.sam # Nanopore Q20 genomic reads (v2.27+) ./minimap2 -ax sr ref.fa read1.fa read2.fa > aln.sam # short genomic paired-end reads ./minimap2 -ax splice ref.fa rna-reads.fa > aln.sam # spliced long reads (strand unknown) ./minimap2 -ax splice -uf -k14 ref.fa reads.fa > aln.sam # noisy Nanopore direct RNA-seq -./minimap2 -ax splice:hq -uf ref.fa query.fa > aln.sam # PacBio Kinnex/Iso-seq or traditional cDNA -./minimap2 -ax splice --junc-bed anno.bed12 ref.fa query.fa > aln.sam # prioritize on annotated junctions +./minimap2 -ax splice:hq -uf ref.fa query.fa > aln.sam # PacBio Kinnex/Iso-seq (RNA-seq) +./minimap2 -ax splice --junc-bed anno.bed12 ref.fa query.fa > aln.sam # use annotated junctions ./minimap2 -ax splice:sr ref.fa r1.fq r2.fq > aln.sam # short-read RNA-seq (r1236 or later) ./minimap2 -cx asm5 asm1.fa asm2.fa > aln.paf # intra-species asm-to-asm alignment ./minimap2 -x ava-pb reads.fa reads.fa > overlaps.paf # PacBio read overlap @@ -39,7 +39,7 @@ man ./minimap2.1 - [Map long noisy genomic reads](#map-long-genomic) - [Map long mRNA/cDNA reads](#map-long-splice) - [Find overlaps between long reads](#long-overlap) - - [Map short accurate genomic reads](#short-genomic) + - [Map short genomic reads](#short-genomic) - [Map short RNA-seq reads](#short-rna-seq) - [Full genome/assembly alignment](#full-genome) - [Advanced features](#advanced)