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dahak-metagenomics
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dahak
benchmarking and containerization of tools for analysis of complex non-clinical metagenomes.
https://dahak-metagenomics.github.io/dahak
BSD 3-Clause "New" or "Revised" License
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Add read filtering and taxonomic classification Snakefiles + singularity
#83
charlesreid1
closed
6 years ago
10
(in progress) Snakemake file for read filtering
#82
charlesreid1
closed
6 years ago
1
(in progress) Snakemake file for taxonomic classification
#81
charlesreid1
closed
6 years ago
1
Mcintyre dataset
#80
brooksph
closed
6 years ago
2
Updating contributing.md to include more detail
#79
brooksph
closed
6 years ago
2
Update link for singularity mirror
#78
brooksph
closed
6 years ago
1
Mcintyre dataset snakefiles
#77
brooksph
closed
6 years ago
1
create top-level organization page?
#76
ctb
closed
6 years ago
1
Updating contributors guidelines to provide more direction
#75
brooksph
closed
6 years ago
2
Email or text notification (feature request)
#74
bluegenes
closed
6 years ago
4
Strategy for testing
#73
charlesreid1
opened
6 years ago
1
permissions problems with fastqc
#72
charlesreid1
closed
6 years ago
2
Updating contribution guidelines
#71
brooksph
closed
6 years ago
1
updated commentary for krona report
#70
brooksph
closed
6 years ago
0
Limiting kaiju to genus-level output
#69
kternus
closed
6 years ago
5
Figures?
#68
kternus
closed
6 years ago
14
Updated path and file navigation
#67
brooksph
closed
6 years ago
0
Read filtering walkthrough
#66
charlesreid1
closed
6 years ago
5
Reducing cloning time
#65
charlesreid1
closed
6 years ago
8
What do we need for a 1.0 release
#64
brooksph
opened
6 years ago
7
Dockerfiles directory
#63
charlesreid1
closed
6 years ago
3
Update workflow instructions
#62
charlesreid1
closed
6 years ago
2
Discussion of Documentation Content & Workflows
#61
charlesreid1
opened
6 years ago
11
How does one run a workflow?
#60
ctb
closed
6 years ago
6
What is 'SBT assembly'?
#59
ctb
closed
6 years ago
2
Compare sourmash gather output: reads v assemblies
#58
brooksph
closed
6 years ago
2
Update instructions in taxonomic classification readme
#57
charlesreid1
closed
6 years ago
0
Create docker image for the osf cli to leverage osf clone functionality
#56
brooksph
closed
6 years ago
6
Kaiju does not output files in taxonomic workflow
#55
charlesreid1
closed
6 years ago
5
Create Snakefile to reproduce analysis with McIntyre Data
#54
brooksph
closed
6 years ago
3
Storing big files (issue-collecting issue)
#53
charlesreid1
opened
6 years ago
0
Does the Snakemake archive feature support singularity?
#52
brooksph
opened
6 years ago
2
Update pull request checklist to mention binary/data diffs
#51
charlesreid1
closed
6 years ago
0
modified getting started instructions
#50
brooksph
closed
6 years ago
7
Expand on README.md file in workflows directory
#49
charlesreid1
closed
6 years ago
0
Create spike-in dataset with Eukaryotic and viral DNA
#48
brooksph
opened
6 years ago
3
Modified contributors and contribution link
#47
brooksph
closed
6 years ago
0
Create read mapping and variant calling snakefile
#46
brooksph
opened
6 years ago
1
Create taxonomic classification snakemake file
#45
charlesreid1
closed
6 years ago
11
Add instructions for getting started with singularity and snakemake
#44
brooksph
closed
6 years ago
2
Use sphinx to build documentation website
#43
brooksph
closed
6 years ago
3
Feature request - Quast visualization with multiqc
#42
brooksph
opened
6 years ago
0
Kaiju docker container
#41
brooksph
closed
6 years ago
4
Versioning containers
#40
brooksph
closed
6 years ago
1
FDA argos database - reference genome assemblies and illumina and pacbio reads
#39
brooksph
opened
7 years ago
0
Gene-level summaries of metagenomes – appropriate for dahak?
#38
sminot
opened
7 years ago
11
[WIP] Added for loops and kaiju instructions
#37
brooksph
closed
7 years ago
1
Kaiju database is corrupted or not in .tgz format
#36
olungu
closed
6 years ago
12
Revert "Revert "[WIP] Code of conduct""
#35
brooksph
closed
7 years ago
1
Revert "[WIP] Code of conduct"
#34
brooksph
closed
7 years ago
0
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