minor

Author: lh3

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)