diff --git a/README.md b/README.md index 4702cfa..d7318c1 100644 --- a/README.md +++ b/README.md @@ -119,6 +119,9 @@ challenging. Users should not expect hifiasm to phase entire chromosomes at the moment. Also, contigs from different parental chromosomes are randomly mixed as it is just not possible to phase across chromosomes with Hi-C. +Hifiasm does not perform scaffolding for now. You need to run a standalone +scaffolder such as SALSA or 3D-DNA to scaffold phased haplotigs. + ### Trio binning When parental short reads are available, hifiasm can also generate a pair of