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Ray -- Parallel genome assemblies for parallel DNA sequencing
http://denovoassembler.sf.net
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remove estimated genome size in Analysis.txt
#48
sebhtml
closed
12 years ago
1
maybe use another way for computePeak in seeds
#47
sebhtml
closed
12 years ago
3
dump seed coverage as XML
#46
sebhtml
closed
11 years ago
1
Ray segfaults only guillimin for ERS006485 (Qin et al. Nature 2010)
#45
sebhtml
closed
12 years ago
4
Ray v1.7. Critial error found
#44
mscook
closed
12 years ago
2
Ray v1.7. Fails to produce scaffolds in hybrid Ill-PE 454-PE assembly. Potential bug where PE-454 data with large inserts is not detected.
#43
mscook
closed
11 years ago
5
Assembler panic: no peak observed in the k-mer coverage distribution.
#42
mscook
closed
12 years ago
1
Scaffolding should not use weak peaks in the distribution of outer distances
#41
sebhtml
closed
12 years ago
7
seg fault with Ray with maxkmerlength 64
#40
sebhtml
closed
12 years ago
2
Compare -k 31 and -k 33 on datasets
#39
sebhtml
closed
11 years ago
1
Don't estimate outer distances when there are no paired reads
#38
sebhtml
closed
12 years ago
1
Hi! I cleaned up your code for you!
#37
GunioRobot
closed
12 years ago
0
add timers to -run-profiler
#36
sebhtml
closed
12 years ago
1
remove persistent code in communication/MessagesHandler.cpp
#35
sebhtml
closed
12 years ago
1
remove persistent code in communication/MessagesHandler.cpp
#34
sebhtml
closed
12 years ago
1
remove dependancy for clock_gettime -- use gettimeofday or GetSystemTime
#33
sebhtml
closed
12 years ago
1
Run with -run-profiler on the Assemblathon-2/Fish dataset and inspect the extension step
#32
sebhtml
closed
12 years ago
1
get Ray to compile with g++ -Werror -Wall -W -Wshadow -fno-common
#31
sebhtml
closed
12 years ago
1
add option -debug-scaffolder
#30
sebhtml
closed
12 years ago
1
remove INLINE from Ray code.
#29
sebhtml
closed
12 years ago
1
RayVersion and RayCommand are not written
#28
sebhtml
closed
12 years ago
1
remove minimumNumberOfRawLinks=3 in Scaffolder
#27
sebhtml
closed
12 years ago
1
improve the scaffolding process
#26
sebhtml
closed
12 years ago
3
dummy task for milestone 1.7
#25
sebhtml
closed
12 years ago
0
add checkpoint ContigPaths
#24
sebhtml
closed
12 years ago
2
Add file ContigVertexCoverage.txt
#23
sebhtml
closed
12 years ago
1
implement case with reverse strand in JoinerWorker
#22
sebhtml
closed
12 years ago
1
change default to ASSERT=y
#21
sebhtml
closed
12 years ago
1
use mpiexec in examples
#20
sebhtml
closed
12 years ago
1
add checkpoint for LibraryLengths
#19
sebhtml
closed
11 years ago
1
m_extended++ is not properly placed in SeedExtender
#18
sebhtml
closed
12 years ago
1
CoverageDistribution is broken for very small genomes (< 100k)
#17
sebhtml
closed
12 years ago
1
Create a LoaderInterface
#16
sebhtml
closed
11 years ago
2
Find out how to generate the change log with git log and tags
#15
sebhtml
closed
12 years ago
1
Port Ray C++ code to the VirtualProcessor
#14
sebhtml
closed
12 years ago
2
reduce memory usage of Kmer objects
#13
sebhtml
closed
12 years ago
1
phix is broken
#12
sebhtml
closed
12 years ago
1
all files written by Ray should go in a directory named after -o
#11
sebhtml
closed
12 years ago
1
cycling is broken
#10
sebhtml
closed
12 years ago
5
Cache messages in extension
#9
sebhtml
closed
12 years ago
0
L1-L3 has too many contigs/nucleotides on guillimin with 512 cores
#8
sebhtml
closed
12 years ago
1
bug: L1-L3 has weird assemblies on 256 cores vs 32 cores.
#7
sebhtml
closed
12 years ago
1
free unused reads in extension
#6
sebhtml
closed
12 years ago
0
implement indel model for PacBio reads and 454 reads
#5
sebhtml
closed
11 years ago
1
recycle/replace wrongly staged read in pairs
#4
sebhtml
opened
12 years ago
1
add running time file
#3
sebhtml
closed
12 years ago
1
checkpoints should be written to RayCheckPoints
#2
sebhtml
closed
12 years ago
3
Colour-space encoder / decoder
#1
gringer
closed
13 years ago
2
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