Recent changes to ComputingTime

ComputingTime modified by Robert Kofler

Robert Kofler — Wed, 27 Apr 2016 16:14:45 -0000

--- v6
+++ v7
@@ -22,6 +22,6 @@

 # Material and Methods for benchmarks
-To measure the computing time of PoPoolationTE2 we used real data published by http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002487
+To measure the computing time of PoPoolationTE2 (v1.09.03) we used real data published by http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002487
 Briefly, 118 isofemale lines were established from a  population of *D. melanogaster* collected 2008 in northern Portugal (Povoa de Varzim). Five females of each line  were combined and sequenced as pool (Pool-Seq). Data are available from ENA (http://www.ebi.ac.uk/ena) with the accession number  SRA035392. Reads were mapped to the *D.melanogaster* reference genome (v5.31) with bwa (v0.7.4) using the bwasw algorithm.
 Time measurements were performed with the following shell script https://sourceforge.net/projects/popoolation-te2/files/publicationrelated/timemeasure-reviewer.sh/download

ComputingTime modified by Robert Kofler

Robert Kofler — Tue, 26 Apr 2016 14:32:17 -0000

--- v5
+++ v6
@@ -2,7 +2,7 @@

 # Benchmarks
-Using 19.5 million paired end fragments (2x76bp) and  *D. melanogaster* as reference  (120Mbp genome) we obtained the following time measurements with PoPoolationTE2.
+With 19.5 million paired end fragments (2x76bp) and  *D. melanogaster* as reference  (120Mbp genome) running PoPoolationTE2 has the following time requirements

 step  | time \[minutes] 
 ---------- | ---------- 
@@ -14,6 +14,7 @@
 estimating strand of TEs | 4.2
 estimating population frequency of TEs |  3.4
 pairing up signatures of TE insertions | 2.4
+    |
 total | 74.1
 total - without mapping (= only  PoPoolationTE2) | 28.1

ComputingTime modified by Robert Kofler

Robert Kofler — Tue, 26 Apr 2016 14:30:11 -0000

--- v4
+++ v5
@@ -6,17 +6,16 @@

 step  | time \[minutes] 
 ---------- | ---------- 
-mapping both reads separately (bwa bwasw) using 12 threads      | 33.45        
+mapping both reads separately (bwa bwasw) using 12 threads      | 33.5       
 restoring paired end information (se2pe)      | 12.5    
-generating a ppileup file | 7.33
+generating a ppileup file | 7.3
 subsampling the ppileup file to a uniform physical coverage| 6.3
-identifying signatures of TE insertions | 4.32
+identifying signatures of TE insertions | 4.3
 estimating strand of TEs | 4.2
-estimating population frequency of TEs |  3.42
-pairing up signatures of TE insertions | 2.36
----------- | ---------- 
-total | bla
-total; without mapping (solely running PoPoolationTE2)
+estimating population frequency of TEs |  3.4
+pairing up signatures of TE insertions | 2.4
+total | 74.1
+total - without mapping (= only  PoPoolationTE2) | 28.1

ComputingTime modified by Robert Kofler

Robert Kofler — Tue, 26 Apr 2016 14:27:50 -0000

--- v3
+++ v4
@@ -8,6 +8,16 @@
 ---------- | ---------- 
 mapping both reads separately (bwa bwasw) using 12 threads      | 33.45        
 restoring paired end information (se2pe)      | 12.5    
+generating a ppileup file | 7.33
+subsampling the ppileup file to a uniform physical coverage| 6.3
+identifying signatures of TE insertions | 4.32
+estimating strand of TEs | 4.2
+estimating population frequency of TEs |  3.42
+pairing up signatures of TE insertions | 2.36
+---------- | ---------- 
+total | bla
+total; without mapping (solely running PoPoolationTE2)
+

ComputingTime modified by Robert Kofler

Robert Kofler — Tue, 26 Apr 2016 14:22:04 -0000

--- v2
+++ v3
@@ -6,7 +6,7 @@

 step  | time \[minutes] 
 ---------- | ---------- 
-mapping both reads (bwa bwasw)      | 33.45        
+mapping both reads separately (bwa bwasw) using 12 threads      | 33.45        
 restoring paired end information (se2pe)      | 12.5

ComputingTime modified by Robert Kofler

Robert Kofler — Tue, 26 Apr 2016 14:21:20 -0000

--- v1
+++ v2
@@ -4,10 +4,10 @@
 # Benchmarks
 Using 19.5 million paired end fragments (2x76bp) and  *D. melanogaster* as reference  (120Mbp genome) we obtained the following time measurements with PoPoolationTE2.

-step  | time [minutes] 
+step  | time \[minutes] 
 ---------- | ---------- 
-mapping (bwasw)      | 33.45        
-se2pe      | 12.5    
+mapping both reads (bwa bwasw)      | 33.45        
+restoring paired end information (se2pe)      | 12.5

ComputingTime modified by Robert Kofler

Robert Kofler — Tue, 26 Apr 2016 14:20:41 -0000

Benchmarks
Material and Methods for benchmarks

Benchmarks

Using 19.5 million paired end fragments (2x76bp) and D. melanogaster as reference (120Mbp genome) we obtained the following time measurements with PoPoolationTE2.

step	time [minutes]
mapping (bwasw)	33.45
se2pe	12.5

Material and Methods for benchmarks

To measure the computing time of PoPoolationTE2 we used real data published by http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002487
Briefly, 118 isofemale lines were established from a population of D. melanogaster collected 2008 in northern Portugal (Povoa de Varzim). Five females of each line were combined and sequenced as pool (Pool-Seq). Data are available from ENA (http://www.ebi.ac.uk/ena) with the accession number SRA035392. Reads were mapped to the D.melanogaster reference genome (v5.31) with bwa (v0.7.4) using the bwasw algorithm.
Time measurements were performed with the following shell script https://sourceforge.net/projects/popoolation-te2/files/publicationrelated/timemeasure-reviewer.sh/download