diff --git a/README.md b/README.md index a64021d..c4fd6d9 100644 --- a/README.md +++ b/README.md @@ -86,10 +86,8 @@ highlighted in bold. ## Limitations -* At the alignment phase, minimap2 performs global alignments between minimizer - hits. If the positions of these minimizer hits are incorrect, the final - alignment may be suboptimal or unnecessarily fragmented. This should happen - rarely with the latest version. +* Minimap2 may produce suboptimal alignments through long low-complexity + regions where seed positions may be inaccurate. * Minimap2 may produce poor alignments that may need post-filtering. We are still exploring a reliable and consistent way to report good alignments. diff --git a/minimap2.1 b/minimap2.1 index ceb2c6c..a4d4ba6 100644 --- a/minimap2.1 +++ b/minimap2.1 @@ -1,4 +1,4 @@ -.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 .PP minimap2 - mapping and alignment between collections of DNA sequences @@ -138,7 +138,7 @@ number of minimizers [3] Discard chains with chaining score .RI < INT [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 .B -X 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 .TP 2 * -At the alignment phase, minimap2 performs global alignments between minimizer -hits. If the positions of these minimizer hits are incorrect, the final -alignment may be suboptimal or unnecessarily fragmented. +Minimap2 may produce suboptimal alignments through long low-complexity regions +where seed positions may be inaccurate. .TP * Minimap2 may produce poor alignments that may need post-filtering. We are still