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Ray -- Parallel genome assemblies for parallel DNA sequencing
http://denovoassembler.sf.net
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checkpoint CoverageDistribution should exist for all ranks
#148
sebhtml
closed
11 years ago
1
Ray reports a problem when file names are too short, but this should work without problem
#147
sebhtml
closed
11 years ago
5
Independent Kmer total in Taxons.xml
#146
fredericraymond
opened
11 years ago
6
debug storage engine (the DHT) with one of the Ray switches on large dataset
#145
sebhtml
closed
11 years ago
2
use 2-bit encoding in GraphPath objects
#144
sebhtml
closed
11 years ago
1
add some meta-information on checkpoints (k-mer length, ranks)
#143
sebhtml
opened
11 years ago
1
path storage using blocks has a bug (not in production)
#142
sebhtml
closed
11 years ago
15
Redundant sequences with bigger k
#141
fredericraymond
closed
11 years ago
11
eliminate invalid paths that originated from weak parts of bubbles
#140
sebhtml
closed
11 years ago
1
adaptative bloom filter
#139
sebhtml
closed
11 years ago
5
store path as sequences instead as of vector of vertices for efficiency
#138
sebhtml
closed
11 years ago
1
add readahead in fastq loader class
#137
sebhtml
closed
11 years ago
4
majority of running time for large samples is dominated by those bubbles
#136
sebhtml
closed
11 years ago
35
This does not make sense: "Estimated remaining time for this step: -8 seconds"
#135
sebhtml
closed
11 years ago
2
Segmentation fault on 2048 MPI ranks
#134
sebhtml
closed
11 years ago
4
Filter automatically obvious false positives in "Ray Communities" using topology
#133
sebhtml
opened
11 years ago
2
compute local coverages during extension to further increase locality
#132
sebhtml
opened
11 years ago
7
reduce amount of information in standard output
#131
sebhtml
closed
11 years ago
3
remove even more information from stdout during the extension
#130
sebhtml
closed
11 years ago
1
remove all calls to fflush
#129
sebhtml
closed
11 years ago
1
reduce verbosity of graph traversal
#128
sebhtml
closed
11 years ago
1
reduce verbosity of seeding algorithms
#127
sebhtml
closed
11 years ago
1
allow more than one pending message in the communication system
#126
sebhtml
closed
11 years ago
1
Missing Scheduling information at 32 cores
#125
sebhtml
closed
11 years ago
5
output 1 single LibraryFrequencies.txt containing Library0.txt, Library1.txt and so on.
#124
sebhtml
closed
11 years ago
1
integer overflow with too many files (4288 files)
#123
sebhtml
closed
11 years ago
4
What is the average coverage in scaffolds ? Maybe use the same used for seeds !
#122
sebhtml
closed
11 years ago
2
what is the peak coverage for extension ? Is it the one of a seed, of the extension, or something else ???
#121
sebhtml
closed
11 years ago
3
need to rework computation of peak (force density to be > 10% on the right of peak)
#120
sebhtml
closed
11 years ago
1
port the scaffolder to the VirtualProcessor framework in RayPlatform
#119
sebhtml
opened
11 years ago
0
graph traversal for a seed should not happen in the other direction as soon as the number of nucleotiodes exceed the largest insert size + 3 times the standard deviation
#118
sebhtml
opened
11 years ago
2
add scaffolder metrics
#117
sebhtml
opened
11 years ago
0
Checkpoints break extension produce shorter sequencers
#116
sebhtml
closed
11 years ago
1
Add header in SeedLengthDistribution.
#115
sebhtml
closed
11 years ago
1
Sometimes there is k-mers with a coverage of 1 with the Bloom filter
#114
sebhtml
closed
10 years ago
8
Add header #Coverage Frequency in Coverage distribution
#113
sebhtml
closed
11 years ago
1
Throw a error message when read count does not match in paired files
#112
sebhtml
closed
10 years ago
1
mini-ranks fail on large jobs, easy to fix
#111
sebhtml
closed
11 years ago
5
Implement a multiplicity engine
#110
sebhtml
opened
11 years ago
2
add ReadLengthDistribution.txt
#109
sebhtml
opened
11 years ago
0
restore MessagePassingInterface.txt (or remove it)
#108
sebhtml
closed
11 years ago
3
Use vertexRank() method everywhere
#107
sebhtml
closed
11 years ago
1
Sometimes, OutputNumbers.txt is incomplete
#106
sebhtml
closed
11 years ago
2
kmers.txt should contain only 1 header
#105
sebhtml
closed
11 years ago
1
-version has extra token
#104
sebhtml
closed
11 years ago
1
Don't put new line in fasta files
#103
sebhtml
closed
11 years ago
3
Missing '.' in file name for Rank9RayExtensions.fasta
#102
sebhtml
closed
11 years ago
1
Missing region in assembly
#101
sebhtml
closed
11 years ago
18
Stability problem with experimental mini-ranks
#100
sebhtml
closed
11 years ago
8
fix -route-messages
#99
sebhtml
closed
11 years ago
6
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