epam/fonda

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Fonda is a framework which offers scalable and automatic analysis of multiple NGS sequencing data types

Stars: 8
Forks: 2
Open beginner issues: 0
Indexed issues: 16

Dominant language: Java
License: Apache-2.0
Last GitHub push: May 25, 2022
Latest indexed: Sep 15, 2026
Contributing guide: Contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

Beginner friendly Everything

Open All

16 open issues indexed

Middleware strategy Open

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

epam/fonda#212 · 1 comment · Opened May 19, 2021
WGS pipeline parallelization Open

draft

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

epam/fonda#202 · Opened Apr 28, 2021
Create new sample mapping strategy for multiomics single cell Open

enhancement

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

epam/fonda#201 · Opened Apr 28, 2021
Combine PicardMarkDuplicate and PicardRemoveDuplicate into single tool Open

dna question

epam/fonda#197 · 1 comment · 1 assignee · Opened Apr 21, 2021
Fix @RG tag in sam/bam file output Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

epam/fonda#196 · Opened Apr 20, 2021
A new Fonda scripting/launching approach Open

draft

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

epam/fonda#162 · 2 comments · Opened Jul 3, 2020
Snpsift tool references in the documentation Open

documentation heritage

Difficulty 2/5 1-3 hours Newbie friendliness 55/100

epam/fonda#145 · Opened May 13, 2020
Exomecnv tool: exome_cnv.R script is not exist Open

bug heritage

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

epam/fonda#143 · Opened May 13, 2020
Sequenza tool: sequenza.R script is not exist Open

bug heritage

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

epam/fonda#142 · Opened May 13, 2020
SnpEff annotation step: `vcf_snpeff_annotation.py` script fails with EOFError Open

bug heritage

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

epam/fonda#141 · Opened May 13, 2020
Bam2Fastq workflow sort and index bam steps fail Open

bug heritage

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

epam/fonda#140 · Opened May 13, 2020
Incorrect Fonda behavior in asynchronous mode Open

bug heritage

Difficulty 3/5 1-2 days Newbie friendliness 38/100

epam/fonda#139 · Opened May 13, 2020
MergeMutation status check doesn't respect mode analysis Open

bug dna heritage

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

epam/fonda#138 · 1 comment · Opened May 13, 2020
Incorrect output expected file from FusionCatcher tool Open

bug heritage

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

epam/fonda#137 · Opened May 13, 2020
Add overall information on the issue/pr management approach Open

documentation enhancement

epam/fonda#136 · 1 assignee · Opened May 12, 2020
"Cloud Pipeline" execution backend Open

enhancement

epam/fonda#32 · 1 assignee · Opened Jan 16, 2020

epam/fonda

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