hapdup reference

krol33 · Nov 22, 2021 · ef4df4f · ef4df4f
1 parent af269a3
commit ef4df4f
Show file tree

Hide file tree

Showing 3 changed files with 13 additions and 0 deletions.
diff --git a/README.md b/README.md
@@ -12,6 +12,10 @@ to large mammalian-scale assemblies. The package represents a complete
 pipeline: it takes raw PacBio / ONT reads as input and outputs polished contigs.
 Flye also has a special mode for metagenome assembly.
 
+Currently Flye will produce collapsed assemblies of diploid genomes, 
+represented by a sigle mosaic haplotype. To recover two phased haplotypes
+consider applying [HapDup](https://github.com/fenderglass/hapdup) after the assembly.
+
 Manuals
 -------
 

diff --git a/docs/FAQ.md b/docs/FAQ.md
@@ -27,6 +27,9 @@ Flye will likely recover alternative haplotypes, but will not phase them.
 Because we do not attempt to reconstruct pseudo-haplotypes,
 this will also reduce the overall contiguity.
 
+For genomes with relatively low heterozygosity, it is now possible to recover two phased haplotypes
+by using [HapDup](https://github.com/fenderglass/hapdup) after the Flye assembly.
+
 Are metagenomes supported?
 --------------------------
 

diff --git a/docs/USAGE.md b/docs/USAGE.md
@@ -207,6 +207,12 @@ longer consensus contigs. The option `--keep-haplotypes` retains
 the alternative paths on the graph, producing less contigouos, but
 more detailed assembly.
 
+### Assembling diploid genomes
+
+Currently Flye will produce collapsed assemblies of diploid genomes, 
+represented by a sigle mosaic haplotype. To recover two phased haplotypes
+consider applying [HapDup](https://github.com/fenderglass/hapdup) after the assembly.
+
 ### Scaffold
 
 Starting from the version 2.9 Flye does not perform scaffolding by default,