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caution that the splice:sr is experimental

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Heng Li
2025-04-04 16:34:40 -04:00
parent cbe8d61ca4
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@@ -21,7 +21,7 @@ cd minimap2 && make
./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 (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 -ax splice:sr ref.fa r1.fq r2.fq > aln.sam # short-read RNA-seq (r1236+; experimental)
./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
./minimap2 -x ava-ont reads.fa reads.fa > overlaps.paf # Nanopore read overlap
@@ -40,7 +40,7 @@ man ./minimap2.1
- [Map long mRNA/cDNA reads](#map-long-splice)
- [Find overlaps between long reads](#long-overlap)
- [Map short genomic reads](#short-genomic)
- [Map short RNA-seq reads](#short-rna-seq)
- [Map short RNA-seq reads (experimental & evolving)](#short-rna-seq)
- [Full genome/assembly alignment](#full-genome)
- [Advanced features](#advanced)
- [Working with >65535 CIGAR operations](#long-cigar)
@@ -231,14 +231,16 @@ be paired if they are adjacent in the input stream and have the same name (with
the `/[0-9]` suffix trimmed if present). Single- and paired-end reads can be
mixed.
#### <a name="short-rna-seq"></a>Map short RNA-seq reads
#### <a name="short-rna-seq"></a>Map short RNA-seq reads (experimental & evolving)
```sh
minimap2 -ax splice:sr ref.fa reads-se.fq > aln.sam # single-end
minimap2 -ax splice:sr ref.fa r1.fq r2.fq > aln.sam # paired-end
```
The new preset `splice:sr` was added between v2.28 and v2.29. It functions
similarly to `sr` except that it performs spliced alignment.
similarly to `sr` except that it performs spliced alignment. Note that this
functionality is ***experiemental*** and evolving. It is better not to use it
for production.
#### <a name="full-genome"></a>Full genome/assembly alignment