Owner

cfe-lab

4 indexed repositories · View on GitHub

MiCall
Pipeline for processing FASTQ data from an Illumina MiSeq to genotype human RNA viruses like HIV and hepatitis C

Python · 21 stars
CFEIntact
A bioinformatics tool for detecting defects in HIV-1 proviral sequences.

Python · 5 stars
bblab-server
Useful tools for HIV research from the Brockman and Brumme Lab at SFU

Python · 0 stars
proviral

Python · 0 stars

Beginner friendly Everything

Open All

Base ORF detection on isoforms Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

cfe-lab/CFEIntact#101 · 1 comment · Opened May 29, 2026
Feature Request: Option to use a custom FASTA file as the alignment reference (e.g., for lab strains like NL4-3) Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 45/100

cfe-lab/CFEIntact#100 · 4 comments · Opened May 26, 2026
Report reverse-complement alignments Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

cfe-lab/CFEIntact#42 · Opened May 16, 2025
Disable/do not consider HCV Open

question

Difficulty 3/5 1-2 days Newbie friendliness 35/100

cfe-lab/MiCall#1288 · 5 comments · Opened May 5, 2025
Large input taking a days to process Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

cfe-lab/MiCall#1285 · 15 comments · Opened Apr 27, 2025
Improve typing in source code Open

dependencies enhancement good first issue python

Difficulty 5/5 Over a week Newbie friendliness 25/100

cfe-lab/CFEIntact#33 · Opened Feb 3, 2025
Decide what to do with coverage reporting in presence of large deletions. Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

cfe-lab/MiCall#1193 · 1 comment · Opened Nov 1, 2024
Simplify comparison of project definitions Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

cfe-lab/MiCall#1158 · Opened Oct 17, 2024
Move to `mappy` Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

cfe-lab/proviral#29 · Opened Jul 30, 2024
Display more regions in `regions.csv` Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 42/100

cfe-lab/CFEIntact#25 · Opened Jul 29, 2024
Add type annotations to Biopython code Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

cfe-lab/CFEIntact#23 · 1 comment · Opened Jul 26, 2024
Improve ORF coordinates detection Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 48/100

cfe-lab/CFEIntact#22 · 2 comments · Opened Jul 25, 2024
Present output in a quality-control manner Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

cfe-lab/CFEIntact#20 · Opened May 29, 2024
A Merger Tool Open

enhancement

cfe-lab/MiCall#1036 · 1 comment · 1 assignee · Opened Feb 12, 2024
Add concordance output statistics Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

cfe-lab/CFEIntact#7 · Opened Oct 3, 2023
Improve coordinate concordance Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

cfe-lab/MiCall#965 · Opened May 19, 2023
Google Analytics Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

cfe-lab/bblab-server#23 · Opened Apr 9, 2023
Clean up submodules Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

cfe-lab/bblab-server#13 · Opened Feb 14, 2023
Resistance run fails on Kive if the input files have already been purged Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

cfe-lab/MiCall#921 · Opened Jan 25, 2023
Upload proviral data into the database Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

cfe-lab/proviral#17 · Opened Jan 24, 2023
Replace wiki with static site Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

cfe-lab/bblab-server#10 · 1 comment · Opened Dec 5, 2022
Proviral upload into QAI fails Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

cfe-lab/MiCall#886 · 1 comment · Opened Nov 7, 2022
Collate outputs in Kive Open

Difficulty 4/5 3-5 days Newbie friendliness 32/100

cfe-lab/MiCall#876 · 1 comment · Opened Oct 5, 2022
Upload HIVSeqinR Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

cfe-lab/MiCall#844 · 1 comment · Opened May 17, 2022
Insertion counts for small insertions that change the reading frame Open

Difficulty 4/5 3-5 days Newbie friendliness 38/100

cfe-lab/MiCall#836 · Opened May 10, 2022
Update or fork tcr-dist submode Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

cfe-lab/bblab-server#5 · 3 comments · Opened Apr 27, 2022
Score alignments? Open

cfe-lab/MiCall#826 · 1 assignee · Opened Mar 30, 2022
Add insertion sequence to nuc.csv and amino.csv Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

cfe-lab/MiCall#768 · Opened Nov 10, 2021
Evidence for joins in contigs Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

cfe-lab/MiCall#764 · 1 comment · Opened Oct 28, 2021
Add coverage plots and scores for non-coding regions Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

cfe-lab/MiCall#725 · Opened Jul 5, 2021
Negative mapped count in QAI Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

cfe-lab/MiCall#719 · Opened Jun 21, 2021
Add aligned_table_precursor.csv Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

cfe-lab/proviral#8 · Opened Apr 26, 2021
Evaluate other assemblers Open

cfe-lab/MiCall#665 · 15 comments · 1 assignee · Opened Jan 18, 2021
unpack_mixtures_and_reverse becomes computationally intractable when sequence has many ambiguous characters Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

cfe-lab/MiCall#637 · 5 comments · Opened Nov 4, 2020
Low-prevalance nucleotide mutations Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

cfe-lab/MiCall#628 · Opened Oct 19, 2020
Explain problems with pTrimmer Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 25/100

cfe-lab/MiCall#566 · Opened May 14, 2020
Align deletions after frame shift Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

cfe-lab/MiCall#558 · Opened Apr 21, 2020
Consider replacing Gotoh alignment algorithm Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

cfe-lab/MiCall#556 · 3 comments · Opened Apr 17, 2020
Test more SARS-CoV-2 samples Open

enhancement

cfe-lab/MiCall#555 · 7 comments · 1 assignee · Opened Apr 15, 2020
Speed up Kive launches Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

cfe-lab/MiCall#514 · Opened Jan 10, 2020
Improve amplicon detector Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 28/100

cfe-lab/MiCall#487 · 1 comment · Opened Dec 4, 2019
Recombinant HIV references Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 25/100

cfe-lab/MiCall#482 · Opened Oct 16, 2019
Display primers on contig coverage diagram Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

cfe-lab/MiCall#478 · Opened Jul 31, 2019
BaseSpace API endpoint stopped working Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

cfe-lab/MiCall#476 · 1 comment · Opened Jul 16, 2019
Split into separate pipelines? Open

question

Difficulty 5/5 Over a week Newbie friendliness 25/100

cfe-lab/MiCall#466 · Opened Apr 3, 2019
Rerun a sample if it gets purged Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

cfe-lab/MiCall#464 · 1 comment · Opened Mar 20, 2019
Report common T-cell receptor sequences Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 42/100

cfe-lab/MiCall#461 · 2 comments · Opened Mar 13, 2019
Some samples not uploaded to QAI Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 15/100

cfe-lab/MiCall#456 · 5 comments · Opened Oct 17, 2018
Validate HCV subtype calls Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

cfe-lab/MiCall#443 · 4 comments · Opened Jun 12, 2018
Score HCV mutation combinations Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

cfe-lab/MiCall#440 · Opened May 14, 2018

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