From 4422c0c6f93ab005874604b7c51575780b0d49eb Mon Sep 17 00:00:00 2001 From: Don Kirkby Date: Fri, 14 May 2021 12:16:12 -0700 Subject: [PATCH 1/4] Typo fix in Python README. Thanks for sharing minimap2. Here's a little fix. --- python/README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 From 10502e2a78dcc7be87b0a3ecb0e70900b386e30a Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Thu, 13 May 2021 17:55:47 +0200 Subject: [PATCH 2/4] Fixed typo in Readme.md deltion -> deletion --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index dafb655..9865b93 100644 --- a/README.md +++ b/README.md @@ -274,7 +274,7 @@ 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. From 2a3793bbd264f241bc79af1793dcf6c839fd9edb Mon Sep 17 00:00:00 2001 From: Heng Li Date: Sun, 23 May 2021 13:08:15 -0400 Subject: [PATCH 3/4] clarify that map-hifi is for HEAD only Resolves #747 --- README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index dafb655..3e5e0bc 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 From cd66777bfbcfe044a0d0b50051244f30404b8185 Mon Sep 17 00:00:00 2001 From: Ariel Erijman Date: Wed, 19 May 2021 13:58:14 -0400 Subject: [PATCH 4/4] small typo --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index bd40bce..10514a8 100644 --- a/README.md +++ b/README.md @@ -254,7 +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