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vdblab
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vdblab-shotgun
Shotgun metagenomic sequencing processing pipeline
MIT License
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Fix/hlatyping
#44
nickp60
closed
1 year ago
0
Add zymo bugs to kraken db
#43
nickp60
closed
1 year ago
1
preprocess: parallelize `get_all_host_reads` rule
#42
funnell
closed
1 year ago
1
Hotfix/schema types
#41
nickp60
closed
1 year ago
0
Release 0.3.2
#40
nickp60
closed
1 year ago
0
Look for opportunities to optimize with job groups
#39
nickp60
opened
1 year ago
0
fix runtime specifications
#38
nickp60
closed
1 year ago
0
Feature/downsample
#37
nickp60
closed
1 year ago
4
Fix host read extraction timeout.
#36
nickp60
closed
1 year ago
0
standard units for runtime
#35
nickp60
closed
1 year ago
5
Release/0.3.0
#34
nickp60
closed
1 year ago
0
Hotfix/catch bad clumpifying
#33
nickp60
closed
1 year ago
0
Hotfix/catch bad clumpifying
#32
nickp60
closed
1 year ago
1
Preprocess rule get_all_host_reads running into LSF time run limit on lilac
#31
funnell
closed
1 year ago
0
output file cleanup
#30
funnell
closed
1 year ago
0
Will human/mouse contamination affect HLA typing?
#29
funnell
opened
1 year ago
0
xHLA is apparently given incompatible bam files
#28
funnell
closed
1 year ago
0
Release/0.2.0
#27
nickp60
closed
1 year ago
0
Consider alternatives for annotation and binning
#26
nickp60
opened
1 year ago
1
Make fall-back output file for xHLA
#25
nickp60
closed
1 year ago
0
Specify specific list of valid platforms
#24
funnell
opened
1 year ago
0
hotfix: deal with our cluster's weird tmpdir rules
#23
nickp60
closed
1 year ago
0
Use snakefmt 0,6,1 until superlinter bumps version and we have to fix everything agin
#22
nickp60
closed
1 year ago
2
Fix/boringcolors
#21
nickp60
closed
1 year ago
0
clean up preprocessing, add host reads and human primary alignment outputs
#20
nickp60
closed
1 year ago
0
add platform to config and option to ignore optical dedup; fix issue #15
#19
nickp60
closed
1 year ago
1
Fix/documentation
#14
nickp60
closed
1 year ago
0
flexible main
#1
nickp60
closed
1 year ago
0
Keep an eye on Seqkit split2
#2
nickp60
opened
1 year ago
0
Files to be deleted
#3
nickp60
opened
2 years ago
10
test data doesn't have enough reads to result in metaphlan hits
#4
nickp60
closed
1 year ago
1
keep an eye on humann bad metaphlan parsing issue
#5
nickp60
opened
2 years ago
0
add option to humann to process paired RNA and DNA
#6
ssraj017
opened
2 years ago
0
confirm whether or not out kraken and metaphlan databases include both rna and dna viruses
#7
nickp60
opened
2 years ago
0
Standardize docker images
#8
funnell
opened
2 years ago
0
alternate HLA typing
#9
nickp60
opened
2 years ago
0
guidance on metaphlan and kraken2 usage
#11
funnell
closed
1 year ago
5
Add in Bhatt lab small orf tool
#10
nickp60
opened
2 years ago
0
add more shotgun virome workflows
#17
funnell
opened
2 years ago
0
Add --RNA option to vdb_shotgun workflow
#18
nickp60
opened
2 years ago
4
vdb_shotgun: add "ordered" flag to bbduk command
#15
funnell
closed
1 year ago
4
vdb_shotgun: consider OGUs
#12
funnell
opened
2 years ago
0
vdb_shotgun: consider mOTUs
#16
funnell
opened
2 years ago
0
vdb_shotgun: automate DAG image creation using GH Actions
#13
funnell
opened
2 years ago
0
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