fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-10-04 20:28:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

documented 2-pass in README

Browse Source
This commit is contained in:
Heng Li
2025-04-13 17:14:44 -04:00
parent 01ccedd5a0
commit ff312a2957
1 changed files with 3 additions and 0 deletions
Download Patch File Download Diff File Expand all files Collapse all files
README.md
+3
View File
@@ -241,6 +241,9 @@ mixed.
minimap2 -ax splice:sr ref.fa reads-se.fq.gz > aln.sam # single-end minimap2 -ax splice:sr ref.fa reads-se.fq.gz > aln.sam # single-end
minimap2 -ax splice:sr ref.fa r1.fq.gz r2.fq.gz > aln.sam # paired-end minimap2 -ax splice:sr ref.fa r1.fq.gz r2.fq.gz > aln.sam # paired-end
minimap2 -ax splice:sr -j anno.bed ref.fa r1.fq r2.fq > aln.sam # use annotation minimap2 -ax splice:sr -j anno.bed ref.fa r1.fq r2.fq > aln.sam # use annotation
# 2-pass alignment
minimap2 -x splice:sr -j anno.bed --write-junc ref.fa r1.fq r2.fq > junc.bed
minimap2 -ax splice:sr -j anno.bed --pass1=junc.bed ref.fa r1.fq r2.fq > aln.sam
``` ```
The new preset `splice:sr` was added between v2.28 and v2.29. It functions The new preset `splice:sr` was added between v2.28 and v2.29. It functions
similarly to `sr` except that it performs spliced alignment. Note that this similarly to `sr` except that it performs spliced alignment. Note that this