diff --git a/Makefile b/Makefile index 984e9a0..2349e50 100644 --- a/Makefile +++ b/Makefile @@ -43,7 +43,7 @@ Assembly.o: kthread.h CommandLines.o: CommandLines.h ketopt.h Correct.o: Correct.h Hash_Table.h htab.h Process_Read.h Overlaps.h kvec.h Correct.o: kdq.h CommandLines.h Levenshtein_distance.h POA.h Assembly.h -Correct.o: ksw2.h +Correct.o: ksw2.h ksort.h Hash_Table.o: Hash_Table.h htab.h Process_Read.h Overlaps.h kvec.h kdq.h Hash_Table.o: CommandLines.h ksort.h Levenshtein_distance.o: Levenshtein_distance.h diff --git a/README.md b/README.md index ac76766..5dd7a5a 100644 --- a/README.md +++ b/README.md @@ -192,4 +192,8 @@ page](https://github.com/chhylp123/hifiasm/issues). ## Limitations -1. Purging haplotig duplications may introduce misassemblies. \ No newline at end of file +1. Purging haplotig duplications may introduce misassemblies. + +## Citation + +Cheng, H., Concepcion, G.T., Feng, X., Zhang, H., Li H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods 18, 170–175 (2021). https://doi.org/10.1038/s41592-020-01056-5