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clarify that wrong seeding mainly occurs in LCRs

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Heng Li
2017-07-28 14:33:15 -04:00
parent ebbe9c1eb8
commit 84922cfe41
2 changed files with 6 additions and 9 deletions
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README.md
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@@ -86,10 +86,8 @@ highlighted in bold.
## Limitations ## Limitations
* At the alignment phase, minimap2 performs global alignments between minimizer * Minimap2 may produce suboptimal alignments through long low-complexity
hits. If the positions of these minimizer hits are incorrect, the final regions where seed positions may be inaccurate.
alignment may be suboptimal or unnecessarily fragmented. This should happen
rarely with the latest version.
* Minimap2 may produce poor alignments that may need post-filtering. We are * Minimap2 may produce poor alignments that may need post-filtering. We are
still exploring a reliable and consistent way to report good alignments. still exploring a reliable and consistent way to report good alignments.
minimap2.1
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.TH minimap2 1 "27 July 2017" "minimap2-2.0-r213-dirty" "Bioinformatics tools" .TH minimap2 1 "28 July 2017" "minimap2-2.0-r219-dirty" "Bioinformatics tools"
.SH NAME .SH NAME
.PP .PP
minimap2 - mapping and alignment between collections of DNA sequences minimap2 - mapping and alignment between collections of DNA sequences
@@ -138,7 +138,7 @@ number of minimizers [3]
Discard chains with chaining score Discard chains with chaining score
.RI < INT .RI < INT
[40]. Chaining score equals the approximate number of matching bases minus a [40]. Chaining score equals the approximate number of matching bases minus a
linear gap penalty. It is computed with dynamic programming. concave gap penalty. It is computed with dynamic programming.
.TP .TP
.B -X .B -X
Perform all-vs-all mapping. In this mode, if the query sequence name is Perform all-vs-all mapping. In this mode, if the query sequence name is
@@ -342,9 +342,8 @@ cg Z CIGAR string (only in PAF)
.SH LIMITATIONS .SH LIMITATIONS
.TP 2 .TP 2
* *
At the alignment phase, minimap2 performs global alignments between minimizer Minimap2 may produce suboptimal alignments through long low-complexity regions
hits. If the positions of these minimizer hits are incorrect, the final where seed positions may be inaccurate.
alignment may be suboptimal or unnecessarily fragmented.
.TP .TP
* *
Minimap2 may produce poor alignments that may need post-filtering. We are still Minimap2 may produce poor alignments that may need post-filtering. We are still