Skip to content

Issues: vdblab/vdblab-shotgun

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

29 Open 21 Closed
29 Open 21 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Issues list

Compress kraken2.out files? good first issue Good for newcomers
#94 opened Sep 23, 2024 by miraep8
Clean up the temporary annotation outputs good first issue Good for newcomers
#93 opened Sep 23, 2024 by miraep8
Trimming: parameter tuning?
#92 opened Sep 16, 2024 by miraep8
3
Host read removal: use human pangenome reference
#89 opened May 21, 2024 by funnell
Can we parse the kmer output of fastqc to estimate de-duplication memory requirements?
#87 opened May 20, 2024 by nickp60
Parallelize some of our bash scripts better
#86 opened May 10, 2024 by miraep8
Concatenate host reference genomes for depletion steps rather than running sequentially enhancement New feature or request
#82 opened Apr 25, 2024 by nickp60
remove shards from assembly for easier importing
#73 opened Jan 8, 2024 by nickp60
add minimizer output to kraken
#72 opened Nov 16, 2023 by nickp60 Version 0.5
Split kraken rule to not run kraken and phanta enhancement New feature or request
#71 opened Nov 7, 2023 by nickp60 Version 0.5
Add entropy filter to bbduk enhancement New feature or request
#70 opened Nov 7, 2023 by nickp60 Version 0.5
1
bowtie_human jobs killed due to hitting memory limit
#63 opened Jun 16, 2023 by funnell
5
Look for opportunities to optimize with job groups
#39 opened Feb 2, 2023 by nickp60
Will human/mouse contamination affect HLA typing?
#29 opened Jan 5, 2023 by funnell
Consider alternatives for annotation and binning
#26 opened Dec 23, 2022 by nickp60
1
Specify specific list of valid platforms
#24 opened Dec 23, 2022 by funnell
Keep an eye on Seqkit split2
#2 opened Dec 8, 2022 by nickp60
Files to be deleted
#3 opened Nov 7, 2022 by nickp60
10
keep an eye on humann bad metaphlan parsing issue
#5 opened Oct 26, 2022 by nickp60
add option to humann to process paired RNA and DNA
#6 opened Oct 4, 2022 by ssraj017
confirm whether or not out kraken and metaphlan databases include both rna and dna viruses
#7 opened Sep 29, 2022 by nickp60
Standardize docker images
#8 opened Sep 23, 2022 by funnell
alternate HLA typing
#9 opened Sep 20, 2022 by nickp60
Add in Bhatt lab small orf tool
#10 opened Sep 15, 2022 by nickp60
add more shotgun virome workflows
#17 opened Aug 25, 2022 by funnell
ProTip! Follow long discussions with comments:>50.