Recent changes to Home

Home modified by Hayan Lee

Hayan Lee — Fri, 21 Nov 2014 06:56:50 -0000

--- v19
+++ v20
@@ -15,7 +15,7 @@
 ***ReadSim v1.6 (Nov, 21, 2014) ***

 * dnasim.py is added. 
-    + dnasim.py simulates polyploidy heterozygous genome. 
+    + dnasim.py simulates heterozygous polyploidy genome. 
     + ./dnasim.py --ploidy 10 --het 0.05 --pre NC_000913 NC_000913.fna
 * pacbio.p5-c3.len.dist file is included.
     + You can use it as a parameter of '--read_dist'.
@@ -49,4 +49,3 @@

 ***ReadSim v1.0 (Nov, 6, 2012) ***

-

Home modified by Hayan Lee

Hayan Lee — Fri, 21 Nov 2014 06:51:37 -0000

--- v18
+++ v19
@@ -14,13 +14,16 @@
 ---
 ***ReadSim v1.6 (Nov, 21, 2014) ***

+* dnasim.py is added. 
+    + dnasim.py simulates polyploidy heterozygous genome. 
+    + ./dnasim.py --ploidy 10 --het 0.05 --pre NC_000913 NC_000913.fna
 * pacbio.p5-c3.len.dist file is included.
     + You can use it as a parameter of '--read_dist'.
     + ./readsim.py sim fq --ref hg19.chr1.fa --pre chr1.c10 --rev_strd off --replace yes --tech pacbio --cov_mu 10 --read_dist pacbio.p5-c3.len.dist
     + This will provide more realistic simulation than {uniform, normal, exp} distribution.
-* dnasim.py is added. 
-    + dnasim.py simulates polyploidy heterozygous genome. 
-    + ./dnasim.py --ploidy 10 --het 0.05 --pre NC_000913 NC_000913.fna
+* Faster!!! Speed is improved
+    + A 4-day job takes only 2 hours!!!
+* timestamp is added

 ***ReadSim v1.5 (Jan, 16, 2013) ***

Home modified by Hayan Lee

Hayan Lee — Fri, 21 Nov 2014 06:20:43 -0000

--- v17
+++ v18
@@ -12,16 +12,25 @@

 Release Notes
 ---
+***ReadSim v1.6 (Nov, 21, 2014) ***
+
+* pacbio.p5-c3.len.dist file is included.
+    + You can use it as a parameter of '--read_dist'.
+    + ./readsim.py sim fq --ref hg19.chr1.fa --pre chr1.c10 --rev_strd off --replace yes --tech pacbio --cov_mu 10 --read_dist pacbio.p5-c3.len.dist
+    + This will provide more realistic simulation than {uniform, normal, exp} distribution.
+* dnasim.py is added. 
+    + dnasim.py simulates polyploidy heterozygous genome. 
+    + ./dnasim.py --ploidy 10 --het 0.05 --pre NC_000913 NC_000913.fna
+
+
 ***ReadSim v1.5 (Jan, 16, 2013) ***

 * Make simulated reads more realistic
     + The option '--read_dist' can take a file, in which each line has a length of a read. File name cannot be {uniform, normal, exp}
-    
     + ./readsim.py sim fq --ref hg19.chr1.fa --pre chr1.c10 --rev_strd off --replace yes --tech perfect --cov_mu 10 --read_dist lens.txt

 ***ReadSim v1.4 (Dec, 3, 2012) ***
-

 * Counting forward/backward reads are added. 
     + (e.g) Total 70593 reads are generated; 40593 is forward, 30000 is reversed
@@ -38,4 +47,3 @@
 ***ReadSim v1.0 (Nov, 6, 2012) ***

-

WikiPage Home modified by Hayan Lee

Hayan Lee — Thu, 17 Jan 2013 14:42:42 -0000

--- v16
+++ v17
@@ -7,6 +7,7 @@

 [[download_button]]

+---

 Release Notes

WikiPage Home modified by Hayan Lee

Hayan Lee — Thu, 17 Jan 2013 14:41:57 -0000

--- v15
+++ v16
@@ -1,6 +1,13 @@
 ReadSim 
 ---
 ReadSim is a fast and simple reads simulator to target long reads such as PacBio or Nanopore.
+
+
+[Manual](manual)
+
+[[download_button]]
+
+

 Release Notes
 ---
@@ -30,11 +37,4 @@
 ***ReadSim v1.0 (Nov, 6, 2012) ***

----

-
-[Manual](manual)
-
-[[download_button]]
-
----

WikiPage Home modified by Hayan Lee

Hayan Lee — Thu, 17 Jan 2013 14:40:43 -0000

--- v14
+++ v15
@@ -29,7 +29,10 @@

 ***ReadSim v1.0 (Nov, 6, 2012) ***

-===
+
+---
+
+
 [Manual](manual)

 [[download_button]]

WikiPage Home modified by Hayan Lee

Hayan Lee — Thu, 17 Jan 2013 14:39:49 -0000

--- v13
+++ v14
@@ -29,6 +29,7 @@

 ***ReadSim v1.0 (Nov, 6, 2012) ***

+===
 [Manual](manual)

 [[download_button]]

WikiPage Home modified by Hayan Lee

Hayan Lee — Thu, 17 Jan 2013 14:39:03 -0000

--- v12
+++ v13
@@ -30,3 +30,7 @@
 ***ReadSim v1.0 (Nov, 6, 2012) ***

 [Manual](manual)
+
+[[download_button]]
+
+---

WikiPage Home modified by Hayan Lee

Hayan Lee — Thu, 17 Jan 2013 14:37:30 -0000

--- v11
+++ v12
@@ -30,5 +30,3 @@
 ***ReadSim v1.0 (Nov, 6, 2012) ***

 [Manual](manual)
-
-[[download_button]]

WikiPage Home modified by Hayan Lee

Hayan Lee — Thu, 17 Jan 2013 14:36:07 -0000

--- v10
+++ v11
@@ -32,7 +32,3 @@
 [Manual](manual)

 [[download_button]]
-
-
-
-