mirror of
https://github.com/lh3/minimap2.git
synced 2026-09-25 14:08:12 +08:00
removed unnecessary empty lines
On linux, these empty lines count.
This commit is contained in:
-13
@@ -64,7 +64,6 @@ ava10k
|
||||
>
|
||||
.I output.paf
|
||||
.RE
|
||||
|
||||
.SH DESCRIPTION
|
||||
.PP
|
||||
Minimap2 is a fast sequence mapping and alignment program that can find
|
||||
@@ -73,11 +72,8 @@ reference genome optionally with detailed alignment (i.e. CIGAR). At present,
|
||||
it works efficiently with query sequences from a few kilobases to ~100
|
||||
megabases in length at a error rate ~15%. Minimap2 outputs in the PAF or the
|
||||
SAM format.
|
||||
|
||||
.SH OPTIONS
|
||||
|
||||
.SS Indexing options
|
||||
|
||||
.TP 10
|
||||
.BI -k \ INT
|
||||
Minimizer k-mer length [17]
|
||||
@@ -111,9 +107,7 @@ Save the minimizer index of
|
||||
to
|
||||
.I FILE
|
||||
[no dump]
|
||||
|
||||
.SS Mapping options
|
||||
|
||||
.TP 10
|
||||
.BI -f \ FLOAT
|
||||
Ignore top
|
||||
@@ -183,9 +177,7 @@ PacBio/Oxford Nanopore read to reference mapping (-Hk19)
|
||||
.B asm1m
|
||||
Long assembly to reference mapping (-k19 -w19)
|
||||
.RE
|
||||
|
||||
.SS Alignment options
|
||||
|
||||
.TP 10
|
||||
.BI -A \ INT
|
||||
Matching score [1]
|
||||
@@ -212,9 +204,7 @@ the contiguity of the alignment at the cost of poor alignment in the middle
|
||||
Minimal peak DP alignment score to output [40]. The peak score is computed from
|
||||
the final CIGAR. It is the score of the max scoring segment in the alignment
|
||||
and may be different from the total alignment score.
|
||||
|
||||
.SS Input/output options
|
||||
|
||||
.TP 10
|
||||
.B -b
|
||||
Generate CIGAR and output alignments in the SAM format. Minimap2 outputs in PAF
|
||||
@@ -232,7 +222,6 @@ takes little CPU time).
|
||||
.TP
|
||||
.B -V
|
||||
Print version number to stdout
|
||||
|
||||
.SH OUTPUT FORMAT
|
||||
.PP
|
||||
Minimap2 outputs mapping positions in the Pairwise mApping Format (PAF) by
|
||||
@@ -257,7 +246,6 @@ _
|
||||
11 int Number bases, including gaps, in the mapping
|
||||
12 int Mapping quality (0-255 with 255 for missing)
|
||||
.TE
|
||||
|
||||
.PP
|
||||
When alignment is available, column 11 gives the total number of sequence
|
||||
matches, mismatches and gaps in the alignment; column 10 divided by column 11
|
||||
@@ -279,7 +267,6 @@ ms i DP score of the max scoring segment in the alignment
|
||||
nn i Number of ambiguous bases in the alignment
|
||||
cg Z CIGAR string (only in PAF)
|
||||
.TE
|
||||
|
||||
.SH SEE ALSO
|
||||
.PP
|
||||
miniasm(1), minimap(1), bwa(1).
|
||||
|
||||
Reference in New Issue
Block a user