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

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16 open issues indexed

"Cloud Pipeline" execution backend Open

enhancement

epam/fonda#32 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Add overall information on the issue/pr management approach Open

documentation enhancement

epam/fonda#136 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Incorrect output expected file from FusionCatcher tool Open

bug heritage

epam/fonda#137 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
MergeMutation status check doesn't respect mode analysis Open

bug dna heritage

epam/fonda#138 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Incorrect Fonda behavior in asynchronous mode Open

bug heritage

epam/fonda#139 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Bam2Fastq workflow sort and index bam steps fail Open

bug heritage

epam/fonda#140 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
SnpEff annotation step: `vcf_snpeff_annotation.py` script fails with EOFError Open

bug heritage

epam/fonda#141 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Sequenza tool: sequenza.R script is not exist Open

bug heritage

epam/fonda#142 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Exomecnv tool: exome_cnv.R script is not exist Open

bug heritage

epam/fonda#143 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Snpsift tool references in the documentation Open

documentation heritage

epam/fonda#145 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
A new Fonda scripting/launching approach Open

draft

epam/fonda#162 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Fix @RG tag in sam/bam file output Open

epam/fonda#196 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Combine PicardMarkDuplicate and PicardRemoveDuplicate into single tool Open

dna question

epam/fonda#197 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Create new sample mapping strategy for multiomics single cell Open

enhancement

epam/fonda#201 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
WGS pipeline parallelization Open

draft

epam/fonda#202 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Middleware strategy Open

epam/fonda#212 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026

epam/fonda

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