cfe-lab/MiCall

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

Stars: 21
Forks: 11
Open beginner issues: 0
Indexed issues: 113
Avg merge: 12h 5m
Merged PRs (30d): 24

Dominant language: Python
License: AGPL-3.0
Last GitHub push: Sep 16, 2026
Latest indexed: Sep 20, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed

Beginner friendly Everything

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113 open issues indexed

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
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
A Merger Tool Open

enhancement

cfe-lab/MiCall#1036 · 1 comment · 1 assignee · Opened Feb 12, 2024
Improve coordinate concordance Open

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

cfe-lab/MiCall#965 · Opened May 19, 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
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
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
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
Mark coverage scores for review Open

enhancement

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

cfe-lab/MiCall#439 · Opened Apr 4, 2018
Generate DOI numbers for each release Open

enhancement

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

cfe-lab/MiCall#434 · Opened Feb 19, 2018
Get key positions from resistance rules Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 30/100

cfe-lab/MiCall#431 · 1 comment · Opened Feb 8, 2018
Mark HCV 7 as not indicated Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 45/100

cfe-lab/MiCall#430 · Opened Jan 15, 2018
Separate HCV 1A from other subtypes Open

enhancement

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

cfe-lab/MiCall#429 · Opened Jan 15, 2018
Try optimizing remap with Cython Open

enhancement

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

cfe-lab/MiCall#426 · Opened Dec 8, 2017
Editing projects.json Open

question

cfe-lab/MiCall#425 · 4 comments · 1 assignee · Opened Dec 5, 2017
Convert coverage plots to SVG Open

enhancement

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

cfe-lab/MiCall#422 · Opened Oct 11, 2017
G2P report on BaseSpace Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 20/100

cfe-lab/MiCall#416 · Opened Sep 8, 2017
Let users add new projects Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 30/100

cfe-lab/MiCall#415 · Opened Sep 6, 2017
Move Virco report into MiCall pipeline Open

enhancement

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

cfe-lab/MiCall#411 · Opened Aug 31, 2017
Improve criteria for when to stop remap iterations Open

enhancement

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

cfe-lab/MiCall#405 · 2 comments · Opened Jun 23, 2017
Move insertions to expected locations Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 28/100

cfe-lab/MiCall#398 · 3 comments · Opened Jun 2, 2017
QAI downloads for gene regions Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 45/100

cfe-lab/MiCall#397 · Opened Jun 1, 2017
Summarize insertions Open

enhancement

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

cfe-lab/MiCall#390 · Opened May 2, 2017
Calculate phiX error rates from Undetermined file Open

enhancement

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

cfe-lab/MiCall#389 · 2 comments · Opened Apr 27, 2017

cfe-lab/MiCall

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