xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-10-10 10:10:56 +08:00
Code Issues Packages Projects Releases Wiki Activity

update r313

Browse Source
This commit is contained in:
chhylp123
2021-03-18 05:26:33 -04:00
parent 3b4953521f
commit 98a04c168a
7 changed files with 62 additions and 177 deletions
Download Patch File Download Diff File Expand all files Collapse all files
hifiasm.1
+3 -7
View File
@@ -286,13 +286,14 @@ times in the other sample.
.TP 10
.BI -l \ INT
Level of purge-dup. 0 to disable purge-dup, 1 to only purge contained haplotigs,
2 to purge all types of haplotigs, 3 to purge all types of haplotigs in most aggressive way.
2 to purge all types of haplotigs, 3 to purge all types of haplotigs in most aggressive way
for high heterozygosity sample.
In default, [2] for non-trio assembly, [0] for trio assembly.
For trio assembly, only level 0 and level 1 are allowed.
.TP
.BI -s \ FLOAT
Similarity threshold for duplicate haplotigs that should be purged [0.75].
Similarity threshold for duplicate haplotigs that should be purged [0.75 for -l1/-l2, 0.55 for -l3].
.TP
.BI -O \ FLOAT
@@ -303,11 +304,6 @@ Min number of overlapped reads for duplicate haplotigs that should be purged [1]
Coverage upper bound of Purge-dups, which is inferred automatically in default.
If the coverage of a contig is higher than this bound, don't apply Purge-dups.
.TP
.BI --high-het \ INT
Enable this mode for high heterozygosity sample, which will increase running time.
For ordinary samples, no need to enable this mode [experimental, not stable].
.SS Debugging options