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broadinstitute
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viral-assemble
viral-ngs: genome assembly and scaffolding
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downsampling of excessive reads
#50
dpark01
opened
1 week ago
0
refine_assembly: tolerate whitespace in fasta headers
#49
dpark01
closed
2 months ago
0
bump viral-core to 2.3.5
#48
dpark01
closed
2 months ago
0
bump viral-core 2.3.2 to 2.3.4
#47
dpark01
closed
2 months ago
0
docbuild fixes, viral-core bump
#46
dpark01
closed
4 months ago
0
update coveralls action; bump actions python to 3.10
#45
tomkinsc
closed
5 months ago
0
skani updates
#44
dpark01
closed
8 months ago
0
expose common parameters for skani at argparse level
#43
dpark01
closed
8 months ago
0
bugfix: make skani dist tolerate empty input
#42
dpark01
closed
8 months ago
0
make reference imputation tolerate incomplete draft assembly input
#41
dpark01
opened
8 months ago
0
bugfix: assemble.skani_contigs_to_refs filtered file was missing header
#40
dpark01
closed
8 months ago
0
skani-based reference selection tools
#39
dpark01
closed
8 months ago
0
update viral-core 2.3.0 -> 2.3.1
#38
tomkinsc
closed
8 months ago
2
build and dependency updates
#37
dpark01
closed
8 months ago
0
add --allow_incomplete_output option to order_and_orient
#36
dpark01
closed
10 months ago
0
update docker base image to v2.2.3 of viral-core; Update conftest.py to account for breaking changes in the newer version of pytest
#35
tomkinsc
closed
1 year ago
0
rename test action in CI
#34
tomkinsc
closed
1 year ago
0
update python modules evaluated for test coverage
#33
tomkinsc
closed
1 year ago
0
Evaluate RagTag for gap filling scaffolded de novo assemblies
#32
tomkinsc
opened
1 year ago
2
addressing documentation build failures; testing ReadTheDocs build check for PRs
#31
tomkinsc
closed
8 months ago
0
migration from Travis CI to GitHub Actions
#30
tomkinsc
closed
1 year ago
0
bump viral-core to 2.1.33
#29
dpark01
closed
1 year ago
0
update SPAdes and default to rnaviralspades settings
#28
dpark01
closed
1 year ago
0
spades: expose more parameters
#27
dpark01
closed
1 year ago
0
fix refine_assembly outVcf when no aligned reads
#26
dpark01
closed
3 years ago
0
bump viral-core to 2.1.16
#25
tomkinsc
closed
3 years ago
0
reactivate integration tests for assembly
#24
dpark01
closed
3 years ago
0
refine_assembly fix for empty reads input
#23
dpark01
closed
3 years ago
0
viral-core 2.1.10 -> 2.1.12 in Dockerfile
#22
tomkinsc
closed
3 years ago
0
remove Trinity tool wrapper, assembly.py::assemble_trinity(), and related unit tests.
#21
tomkinsc
closed
4 years ago
0
remove usage of deprecated Bio.Alphabet
#20
tomkinsc
closed
4 years ago
0
viral-core:2.1.9 -> viral-core:2.1.10
#19
tomkinsc
closed
4 years ago
0
update viral-core 2.1.8->2.1.9
#18
tomkinsc
closed
4 years ago
0
realign to deambig in denovo
#17
tomkinsc
closed
4 years ago
0
bump viral-core image 2.1.4 -> 2.1.8
#16
tomkinsc
closed
4 years ago
0
viral-core 2.1.4
#15
dpark01
closed
4 years ago
0
add alignment_summary script
#14
dpark01
closed
4 years ago
0
bump viral-core
#13
dpark01
closed
4 years ago
0
viral-core 2.1.0 -> 2.1.1
#12
tomkinsc
closed
4 years ago
0
viral-core:2.0.21 - > 2.1.0
#11
tomkinsc
closed
4 years ago
0
mafft 7.402 -> 7.464
#10
tomkinsc
closed
4 years ago
0
viral-core to v2.0.21
#9
tomkinsc
closed
4 years ago
0
viral-core 2.0.17 -> 2.0.18
#8
tomkinsc
closed
4 years ago
0
bump viral-core docker
#7
dpark01
closed
4 years ago
0
bump docker base image; viral-core 2.0.15->2.0.16
#6
tomkinsc
closed
4 years ago
0
bump docker base image; viral-core 2.0.14->2.0.15
#5
tomkinsc
closed
4 years ago
0
doc fixes
#4
dpark01
closed
5 years ago
0
add doc build
#3
dpark01
closed
5 years ago
0
rework
#2
dpark01
closed
5 years ago
0
bump viral-core to 2.0.1
#1
dpark01
closed
5 years ago
0
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