0.16.0 release

docs/source/conf.py

@@ -38,9 +38,9 @@ copyright = u'2021, Haoyu Cheng, Heng Li'
 # built documents.
 #
 # The short X.Y version.
-version = '0.15.5-r350'
+version = '0.16.0-r369'
 # The full version, including alpha/beta/rc tags.
-release = '0.15.5'
+release = '0.16.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/source/faq.rst

@@ -44,7 +44,7 @@ Why one Hi-C integrated assembly is larger than another one?
     Another possibility is that hifiasm misidentifies coverage threshold for homozygous reads. For instance, hifiasm prints the following information during assembly: 
     ::
 
-        [M::purge_dups] purge duplication coverage threshold: 36
+        [M::purge_dups] homozygous read coverage threshold: 36
 
     In this example, hifiasm identifies the coverage threshold for homozygous reads as ``36``. If it is significantly smaller than the homozygous coverage peak, hifiasm will generate two unbalanced assemblies. In this case, please set ``--hom-cov`` to homozygous coverage peak. Please note that tuning ``--hom-cov`` may affect ``*p_utg*gfa`` so that ``*hic*.bin`` should be deleted. Since v0.15.5, hifiasm can detect such changes and renew Hi-C bin files automatically.
 
@@ -60,7 +60,7 @@ For Hi-C integrated assembly, why the assembly size of both haplotypes are much
     If most bases of a diploid sample are homozygous, the coverage threshold is wrongly determined by hifiasm. For instance, hifiasm prints the following information during assembly: 
     ::
 
-        [M::purge_dups] purge duplication coverage threshold: 36
+        [M::purge_dups] homozygous read coverage threshold: 36
 
     In this example, hifiasm identifies the coverage threshold for homozygous reads as ``36``. If it is much smaller than homozygous coverage peak, hifiasm thinks most reads are homozygous and assign them to both assemblies, making both of them much larger than the estimated haploid genome size. In this case, please set ``--hom-cov`` to homozygous coverage peak. Please note that tuning ``--hom-cov`` may affect ``*p_utg*gfa`` so that ``*hic*.bin`` should be deleted. Since v0.15.5, hifiasm can detect such changes and renew Hi-C bin files automatically.
 

docs/source/parameter-reference.rst

@@ -98,6 +98,17 @@ Error correction options
 **\-z <INT=0>**
   Length  of  adapters that should be removed. This option remove ``INT`` bases from both ends of each read.  Some old HiFi reads may consist of short adapters (e.g. 20bp adapter at one end). For such data, trimming short adapters would significantly improve the assembly quality.
 
+.. _max-kocc-opt:
+
+**\-\-max-kocc <INT=2000>**
+  Employ k-mers occurring < ``INT`` times to rescue repetitive overlaps. This option may improve the resolution of repeats.
+
+
+.. _hg-size-opt:
+
+**\-\-hg-size <INT(k/m/g)>**
+  Estimated haploid genome size used for inferring read coverage. This option is used to get accurate homozygous read coverage during error correction. Common suffices are required, for example, 100m or 3g.
+
 
 .. _min-hist-cnt-opt: