Owner

gbouras13

7 indexed repositories · View on GitHub

pharokka
Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.

Python · 231 stars
phold
Phage Annotation using Protein Structures

Python · 175 stars
hybracter
Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.

Python · 156 stars
dnaapler
Reorients assembled microbial sequences

Python · 146 stars
plassembler
Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates

Python · 90 stars
baktfold
Rapid & standardized genome annotation using protein structural information

Python · 79 stars
pypolca
Standalone Python re-implementation of the POLCA polisher from MaSuRCA

Python · 48 stars

Beginner friendly Everything

Open All

Fix Aragorn negative coordinate issue Open

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

gbouras13/pharokka#444 · Opened Sep 17, 2026
`write_genbank` aborts the whole run on a feature BioPython could not place (`AttributeError: 'NoneType' object has no attribute 'start'`) Open

Difficulty 2/5 1-3 hours Newbie friendliness 85/100

gbouras13/phold#141 · Opened Sep 17, 2026
Error with "write feature tsv" Open

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

gbouras13/baktfold#40 · 1 comment · Opened Sep 15, 2026
[BUG] Hybracter stuck on snakemake command for 5 days Open

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

gbouras13/hybracter#168 · Opened Sep 14, 2026
[BUG] pypolca issue Open

Difficulty 2/5 1-3 hours Newbie friendliness 68/100

gbouras13/hybracter#167 · 7 comments · Opened Sep 10, 2026
[BUG] can't run in shared read-only conda env Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

gbouras13/hybracter#166 · 1 comment · Opened Aug 31, 2026
explore adding evades db of anti defence protein structures Open

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

gbouras13/phold#138 · Opened Aug 28, 2026
add .tbl output like pharokka Open

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

gbouras13/phold#137 · Opened Aug 26, 2026
Should you rotate your genome before or after polishing? Open

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

gbouras13/dnaapler#107 · Opened Aug 6, 2026
[BUG] Hybracter hybrid generating large SAM intermediate files during processing Open

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

gbouras13/hybracter#165 · Opened Jul 23, 2026
[BUG] Hybracter apptainer singularity version 1.14.0 error with contaminants.yaml Open

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

gbouras13/hybracter#163 · 2 comments · Opened Jul 20, 2026
Bug report: Potential annotation bug after genome rotation Open

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

gbouras13/pharokka#431 · Opened Jul 2, 2026
[Question] - What happens when assemblies with bona fide linear chromosomes are used as input? Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

gbouras13/dnaapler#105 · 4 comments · Opened Jun 29, 2026
Problem in Singularity Container building - Medaka Open

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

gbouras13/hybracter#159 · 2 comments · Opened Jun 23, 2026
add json -> other outputs recreation command Open

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

gbouras13/baktfold#37 · Opened Jun 16, 2026
Container installation issues[BUG] Open

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

gbouras13/hybracter#158 · 4 comments · Opened Jun 10, 2026
Overlapping Genes Open

question

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

gbouras13/pharokka#429 · 2 comments · Opened May 28, 2026
[BUG] --auto flag fails on macOS ARM64 with spaces injected around sample name in lrge_estimated_chromosome_size.txt path Open

Difficulty 4/5 3-5 days Newbie friendliness 52/100

gbouras13/hybracter#155 · Opened May 20, 2026
Feature request: Change the direction of #labels to horizontal Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

gbouras13/pharokka#428 · Opened May 5, 2026
Lost plasmids Open

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

gbouras13/hybracter#154 · Opened Apr 8, 2026
Inquiry on phold remote Open

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

gbouras13/phold#122 · 1 comment · Opened Mar 16, 2026
crash exit when the custom database finds no hits (bug report) Open

Difficulty 2/5 1-3 hours Newbie friendliness 52/100

gbouras13/phold#121 · Opened Feb 11, 2026
ProstT5 issue submitting job with GPU on HPC Open

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

gbouras13/phold#119 · 3 comments · Opened Feb 2, 2026
Issue regarding negative location values. Open

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

gbouras13/pharokka#418 · 1 comment · Opened Jan 15, 2026
Alternate coding table functionality is broken Open

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

gbouras13/pharokka#417 · 3 comments · Opened Jan 9, 2026
macOS (M-series) install failing / unstable due to NumPy 2.x & PyTorch / Transformers incompatibilities Open

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

gbouras13/phold#112 · 1 comment · Opened Dec 10, 2025
Question Regarding Plasmid Copy Number Calculation Open

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

gbouras13/plassembler#71 · 1 comment · Opened Jun 24, 2025
Update PLSDB version to include archaeal plasmids Open

enhancement

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

gbouras13/plassembler#62 · 10 comments · 1 reaction · Opened May 13, 2025
An error is reported in the hybracter test Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 30/100

gbouras13/hybracter#126 · 1 comment · Opened Feb 20, 2025
Workaround for bacteria with multiple chromosomes Open

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

gbouras13/hybracter#124 · 3 comments · Opened Feb 15, 2025
Interpreting inconsistencies with VFDB annotations between Pharokka and Phold Open

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

gbouras13/phold#82 · 1 comment · Opened Feb 3, 2025
The top terL MMseqs2 hit did not have a MMseqs2 alignment beginning with a valid start codon M, V or L. Open

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

gbouras13/dnaapler#93 · 1 comment · Opened Jan 24, 2025
Question- have you tested pypolca with multiple rounds of polishing? Open

question

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

gbouras13/pypolca#24 · 1 comment · Opened Dec 14, 2024
Feature Request: Proteomics Data Open

enhancement

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

gbouras13/pharokka#367 · Opened Nov 13, 2024
Feature request: Support for linear bacterial replicons? Open

enhancement

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

gbouras13/dnaapler#82 · 12 comments · Opened Oct 21, 2024
Unicycler not found error Open

bug

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

gbouras13/hybracter#102 · 7 comments · Opened Oct 17, 2024
.gfa output file not a typical gfa format Open

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

gbouras13/plassembler#56 · 1 comment · Opened Oct 17, 2024
ValueError: Duplicate key (while no duplicated ids in input) Open

bug

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

gbouras13/pharokka#361 · 2 comments · Opened Oct 4, 2024
Two chromosome contigs in Klebsiella pneumoniae 'chromosome.fasta' file Open

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

gbouras13/plassembler#55 · 5 comments · Opened Sep 23, 2024
Set no/low coverage regions of short reads to N Open

enhancement

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

gbouras13/pypolca#22 · 1 comment · Opened Aug 21, 2024
Mamba not detected with snakemake Open

bug

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

gbouras13/hybracter#85 · 10 comments · Opened Aug 14, 2024
Support reorientation of as many contigs as possible Open

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

gbouras13/dnaapler#80 · Opened Aug 12, 2024
Samtools check validation - ascii error Open

Difficulty 2/5 1-3 hours Newbie friendliness 48/100

gbouras13/pypolca#20 · 1 comment · Opened Aug 2, 2024
extra dependencies :: canu, dnaapler forgotten Open

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

gbouras13/plassembler#54 · 1 reaction · Opened Jul 12, 2024
Can this program be run on an external hard drive? Open

bug

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

gbouras13/hybracter#83 · 4 comments · Opened Jul 2, 2024
Issues with pharokka_multiplotter.py: IndexError: index -1 is out of bounds for axis 0 with size 0 Open

bug

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

gbouras13/pharokka#348 · 3 comments · Opened Jun 24, 2024
Plassembler stops at Processing Sam/Bam Files and extracting Fastqs Open

bug

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

gbouras13/plassembler#53 · 4 comments · Opened May 13, 2024
Error: the assembly_1 and assembly_2 assemblies need to contain the same number of sequences Open

bug

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

gbouras13/hybracter#78 · 1 comment · Opened May 12, 2024
[Feature request] Open

enhancement

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

gbouras13/hybracter#77 · Opened May 6, 2024
PermissionError in `phold plot` Open

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

gbouras13/phold#36 · 6 comments · Opened Apr 12, 2024

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