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sanger-pathogens
/
iva
de novo virus assembler of Illumina paired reads
http://sanger-pathogens.github.io/iva/
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samtools errors caused by mapping.py
#59
koppk
closed
8 years ago
4
pysam 0.9.0
#58
martinghunt
closed
8 years ago
0
Support samtools 1.3
#57
martinghunt
closed
8 years ago
0
IVA: error: unrecognized arguments: path_to_output_directory
#56
george-githinji
closed
8 years ago
4
Kmc threads
#55
martinghunt
closed
8 years ago
0
thread option not passed to kmc
#54
andreas-wilm
closed
8 years ago
3
support an explicit output argument
#53
george-githinji
closed
9 years ago
2
Check samtools version
#52
martinghunt
closed
9 years ago
0
Use pyfastaq 3.10.0
#51
martinghunt
closed
9 years ago
0
import stat required to stop --add_to_ref dying
#50
martinghunt
closed
9 years ago
0
Make tests pass from last merge
#49
martinghunt
closed
9 years ago
0
No strand bias trim
#48
martinghunt
closed
9 years ago
0
version bump, tweak setup.py
#47
martinghunt
closed
9 years ago
0
Die nicely if input reads bad, or when no contigs made
#46
martinghunt
closed
9 years ago
0
Bug reusing bad kmers
#45
martinghunt
closed
9 years ago
0
Bug fix - min contig length now implemented properly
#44
martinghunt
closed
9 years ago
0
Increment version
#43
martinghunt
closed
9 years ago
0
Qc input checks
#42
martinghunt
closed
9 years ago
0
Fix gage bugs
#41
martinghunt
closed
9 years ago
0
No really, make all ratt script executable
#40
martinghunt
closed
9 years ago
0
bug fix running ratt scripts
#39
martinghunt
closed
9 years ago
0
Remove info that is on the gh-pages site
#38
martinghunt
closed
9 years ago
0
Change to pyfastaq
#37
martinghunt
closed
9 years ago
0
Change default extension parameters, bump to version 0.11.0
#36
martinghunt
closed
9 years ago
0
Allow gage to fail as long as we got the stats; v0.10.3
#35
martinghunt
closed
9 years ago
0
version 0.10.2
#34
martinghunt
closed
9 years ago
0
Bug fixes: string decoding and qc write contigs file
#33
martinghunt
closed
9 years ago
0
Link to the pathogens VM
#32
martinghunt
closed
9 years ago
0
Improve read trimming; version 0.10.0
#31
martinghunt
closed
9 years ago
0
version 0.9.0
#30
martinghunt
closed
10 years ago
0
write contigs that do not match reference
#29
martinghunt
closed
10 years ago
0
Add ubuntu installation wiki link
#28
martinghunt
closed
10 years ago
0
Contig trim
#27
martinghunt
closed
10 years ago
0
Pcr primer
#26
martinghunt
closed
10 years ago
0
Added AUTHORS file
#25
aslett1
closed
10 years ago
0
Version 0.5.0
#24
martinghunt
closed
10 years ago
0
Qc cleanup
#23
martinghunt
closed
10 years ago
0
Change default QC percent identities to 80
#22
martinghunt
closed
10 years ago
0
Die gracefully if cannot find reference
#21
martinghunt
closed
10 years ago
0
Add test embl files
#20
martinghunt
closed
10 years ago
0
merge tidy_up_for_v0.4.0
#19
martinghunt
closed
10 years ago
0
merge add_custom_ref_to_db
#18
martinghunt
closed
10 years ago
0
Tidy up checking external programs OK
#17
martinghunt
closed
10 years ago
0
Add citation for adapter sequences
#16
martinghunt
closed
10 years ago
0
Don't write final ORFs file
#15
martinghunt
closed
10 years ago
0
Delete gage-validation.tar.gz
#14
martinghunt
closed
10 years ago
0
Keep gage and ratt code and adapters.fasta files when installing
#13
martinghunt
closed
10 years ago
0
Add checks for external programs in qc scripts
#12
martinghunt
closed
10 years ago
0
Run kraken on reads sampled uniformly across assembly
#11
martinghunt
closed
10 years ago
0
Add QC info and citations
#10
martinghunt
closed
10 years ago
0
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