diff --git a/README.md b/README.md index dafb655..10514a8 100644 --- a/README.md +++ b/README.md @@ -14,7 +14,8 @@ 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 +./minimap2 -ax asm20 ref.fa pacbio-ccs.fq.gz > aln.sam # PacBio HiFi/CCS genomic reads (v2.18) +./minimap2 -ax map-hifi ref.fa pacbio-ccs.fq.gz > aln.sam # PacBio HiFi/CCS genomic reads (GitHub HEAD) ./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 @@ -253,7 +254,7 @@ To avoid this issue, you can add option `-L` at the minimap2 command line. This option moves a long CIGAR to the `CG` tag and leaves a fully clipped CIGAR at the SAM CIGAR column. Current tools that don't read CIGAR (e.g. merging and sorting) still work with such BAM records; tools that read CIGAR will -effectively ignore these records. It has been decided that future tools will +effectively ignore these records. It has been decided that future tools will seamlessly recognize long-cigar records generated by option `-L`. **TL;DR**: if you work with ultra-long reads and use tools that only process @@ -274,7 +275,7 @@ CGATCGATAAATAGAGTAG---GAATAGCA CGATCG---AATAGAGTAGGTCGAATtGCA ``` is represented as `:6-ata:10+gtc:4*at:3`, where `:[0-9]+` represents an -identical block, `-ata` represents a deltion, `+gtc` an insertion and `*at` +identical block, `-ata` represents a deletion, `+gtc` an insertion and `*at` indicates reference base `a` is substituted with a query base `t`. It is similar to the `MD` SAM tag but is standalone and easier to parse. diff --git a/python/README.rst b/python/README.rst index 3d0fae8..3082980 100644 --- a/python/README.rst +++ b/python/README.rst @@ -144,7 +144,7 @@ properties: * **mlen**: length of the matching bases in the alignment, excluding ambiguous base matches. -* **NM**: number of mismatches, gaps and ambiguous poistions in the alignment +* **NM**: number of mismatches, gaps and ambiguous positions in the alignment * **trans_strand**: transcript strand. +1 if on the forward strand; -1 if on the reverse strand; 0 if unknown