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a-ludi
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djunctor
Close assembly gaps using long-reads with focus on correctness.
MIT License
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Reduce number of consensus computations
#58
a-ludi
opened
5 years ago
0
Concise logging rules
#57
a-ludi
opened
5 years ago
0
Testing: insert real Illumina gaps into PacBio assembly
#56
a-ludi
closed
5 years ago
1
User may select a block of the reference DB
#55
a-ludi
closed
5 years ago
1
Users must provide initial alignment
#54
a-ludi
closed
5 years ago
0
Add option to enable extensions
#53
a-ludi
closed
5 years ago
0
Take complementary alignment into account when assembling contigs
#52
a-ludi
closed
6 years ago
1
Require a minimum coverage in pile ups before consensus
#51
a-ludi
opened
6 years ago
0
Filtering for `isValid` discard good reads
#50
a-ludi
closed
5 years ago
0
Is the self-alignment essential?
#49
a-ludi
opened
6 years ago
0
Initialize repeat mask with user input
#48
a-ludi
closed
6 years ago
0
Make main algorithm one-pass-only
#47
a-ludi
closed
6 years ago
1
Move loop structure out of the main algorithm
#46
a-ludi
closed
6 years ago
0
Favor direct sequential output
#45
a-ludi
closed
6 years ago
0
`getComplementaryOrder` should not combine all local alignments into one
#44
a-ludi
closed
6 years ago
0
Weakly anchored alignment chains should not be used for pile ups
#43
a-ludi
closed
6 years ago
1
Select only proper reads as candidates
#42
a-ludi
closed
6 years ago
0
Option to output the set of filtered reads
#41
a-ludi
closed
6 years ago
1
Alignment coverage for detection of "bad" loci
#40
a-ludi
closed
6 years ago
2
Choose error tolerance for self-alignment such that all relevant repeats will be detected
#39
a-ludi
closed
6 years ago
1
Collection of true pile ups might be faulty
#38
a-ludi
closed
6 years ago
1
Provide generated masks outside of the working directory
#37
a-ludi
closed
6 years ago
0
Fix masking of repetitive regions
#36
a-ludi
closed
6 years ago
1
Do not exclude reads with short repeats included
#35
a-ludi
closed
6 years ago
4
Separation of concerns: when to classify as `cat_useless`
#34
a-ludi
closed
6 years ago
0
How long must an anchor be to have high probability of being unique?
#33
a-ludi
opened
6 years ago
0
Require minimum extension length
#32
a-ludi
opened
6 years ago
0
Avoid using two LAS files for the same alignment (`-C` option)
#31
a-ludi
closed
6 years ago
0
`LAdump`: Inverse-order alignment chains might differ from original order chains
#30
a-ludi
closed
6 years ago
2
Improve pre-consensus alignment
#29
a-ludi
opened
6 years ago
0
Make estimate read error rate configurable
#28
a-ludi
closed
6 years ago
0
Eliminate negative gaps
#27
a-ludi
opened
6 years ago
0
Select "good" reads
#26
a-ludi
opened
6 years ago
0
Assess repeat structure
#25
a-ludi
closed
6 years ago
1
Mask low complexity regions
#24
a-ludi
opened
6 years ago
0
`LAdump`: total number of diffs is not sum of trace point diffs
#23
a-ludi
opened
6 years ago
2
How much coverage should you aim for?
#22
a-ludi
opened
6 years ago
0
How does consensus handle hablotypic scenarios?
#21
a-ludi
closed
6 years ago
0
Testing: use two versions of a real genome
#20
a-ludi
opened
6 years ago
0
How to handle scaffold headers?
#19
a-ludi
opened
6 years ago
0
Random batch tests
#18
a-ludi
opened
6 years ago
0
Crop pile up to gap
#17
a-ludi
closed
6 years ago
0
Clean Up OverlayDB
#16
a-ludi
closed
6 years ago
1
Merge OverlayDB
#15
a-ludi
closed
6 years ago
0
Transfer gap closing procedure to sequence extension
#14
a-ludi
closed
6 years ago
0
Potential internal bug of damapper
#13
a-ludi
opened
6 years ago
0
Consider "addressed end" of reference contigs
#12
a-ludi
closed
6 years ago
1
Use extending reads to improve consensus for gaps
#11
a-ludi
closed
6 years ago
2
Fix handling of workdir in `dazzler.d`
#10
a-ludi
closed
6 years ago
0
Preserve input scaffolds
#9
a-ludi
closed
6 years ago
2
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