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32 repositories

mrub-intron-analysis
Public
Jupyter Notebook
•
MIT License
•0•0•2•0•Updated Mar 3, 2026Mar 3, 2026
mrub-sorted-asm
Public
Assembly of Mesodinium rubrum sorted nuclei genomic long read libraries
genome-assembly snakemake-workflow mesodinium
genome-assembly snakemake-workflow mesodinium
Python
•0•1•0•0•Updated Mar 3, 2026Mar 3, 2026
loxodes-nucleosomes-workflow
Public
nucleosome-positioning snakemake-workflow loxodes
nucleosome-positioning snakemake-workflow loxodes
Jupyter Notebook
•
MIT License
•0•0•0•0•Updated Apr 13, 2025Apr 13, 2025
mrub-sorted-compare
Public
Comparison of sorted MIC vs MAC genome assemblies for Mesodinium rubrum
genome-assembly snakemake-workflow mesodinium
genome-assembly snakemake-workflow mesodinium
Python
•0•1•1•0•Updated Jun 11, 2024Jun 11, 2024
loxodes-bleties-workflow
Public
genome-assembly snakemake-workflow loxodes
genome-assembly snakemake-workflow loxodes internal-eliminated-sequences
Jupyter Notebook
•
MIT License
•0•0•0•0•Updated May 6, 2024May 6, 2024
DevPF_code
Public
Jupyter Notebook
•
BSD 2-Clause "Simplified" License
•0•0•0•0•Updated Jan 29, 2024Jan 29, 2024
loxodes-assembly-workflow
Public
genome-assembly snakemake-workflow loxodes
genome-assembly snakemake-workflow loxodes
Python
•
MIT License
•0•0•0•0•Updated Nov 10, 2023Nov 10, 2023
pogigwasc-utils
Public
scripts gene-prediction
scripts gene-prediction
Python
•
MIT License
•0•0•1•0•Updated Nov 10, 2023Nov 10, 2023
eugene
Public
Eugene is an integrative genome annotation software
C++
•1•0•0•0•Updated Oct 30, 2023Oct 30, 2023
trf_utils
Public
Scripts to reformat TRF output files
Python
•
MIT License
•0•0•0•0•Updated Oct 25, 2023Oct 25, 2023
loxodes-srna-workflow
Public
small RNA library processing and analysis
srna snakemake-workflow loxodes
srna snakemake-workflow loxodes
Python
•
MIT License
•0•0•0•0•Updated Oct 25, 2023Oct 25, 2023
loxodes-pogigwasc-workflow
Public
Pogigwasc gene prediction of Loxodes magnus genome
genome-annotation gene-prediction snakemake-workflow
genome-annotation gene-prediction snakemake-workflow loxodes
Python
•
MIT License
•0•0•0•0•Updated Oct 25, 2023Oct 25, 2023
loxodes-kmer-comp
Public
genomics snakemake-workflow loxodes
genomics snakemake-workflow loxodes
Jupyter Notebook
•
MIT License
•0•0•0•0•Updated Oct 25, 2023Oct 25, 2023
loxodes-intronarrator-workflow
Public
Empirical intron annotation for Loxodes magnus genome assembly
genome-annotation snakemake-workflow intron-prediction
genome-annotation snakemake-workflow intron-prediction loxodes
Python
•
MIT License
•0•0•0•0•Updated Oct 25, 2023Oct 25, 2023
mnutils
Public
MNase-seq utilities
nucleosome-positioning
nucleosome-positioning
Python
•
MIT License
•0•0•0•0•Updated Oct 25, 2023Oct 25, 2023
ICOP_code
Public
Software for analysis of data associated with investigations of Paramecium ICOP proteins
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•0•0•1•0•Updated Aug 9, 2023Aug 9, 2023
Intronarrator
Public
Gene prediction using empirically determined introns
gene prediction introns
gene prediction introns
Python
•
BSD 2-Clause "Simplified" License
•0•3•1•0•Updated Oct 14, 2022Oct 14, 2022
pogigwasc
Public
Prediction of genes in genomes with ambiguous stop codons
genetic-code gene-prediction
genetic-code gene-prediction
Java
•
MIT License
•0•2•1•0•Updated Sep 28, 2022Sep 28, 2022
IES_nuc_density
Public
Scripts and notebook for analysis IES nucleosome densities
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•0•0•1•0•Updated Sep 13, 2022Sep 13, 2022
hisat2
Public
Graph-based alignment (Hierarchical Graph FM index)
C++
•
GNU General Public License v3.0
•130•0•0•0•Updated Aug 18, 2022Aug 18, 2022
karyocode-analysis-busco
Public
genetic-code snakemake-workflow karyocode
genetic-code snakemake-workflow karyocode
Shell
•0•0•0•0•Updated Jul 21, 2022Jul 21, 2022
bleties-test-tthe
Public
Benchmarking BleTIES with Tetrahymena long read data
genome-editing internal-eliminated-sequences bleties
genome-editing internal-eliminated-sequences bleties
Jupyter Notebook
•0•0•0•0•Updated Jun 15, 2022Jun 15, 2022
bleties-test-ptet
Public
Benchmarking BleTIES with simulated long reads
genome-editing internal-eliminated-sequences bleties
genome-editing internal-eliminated-sequences bleties
Jupyter Notebook
•0•0•0•0•Updated Jun 15, 2022Jun 15, 2022
karyocode-analysis-porc
Public
genetic-code snakemake-workflow karyocode
genetic-code snakemake-workflow karyocode
Python
•0•0•0•0•Updated Jun 15, 2022Jun 15, 2022
karyocode-workflow
Public
genetic-code snakemake-workflow karyocode
genetic-code snakemake-workflow karyocode
Python
•0•0•0•0•Updated Jun 15, 2022Jun 15, 2022
bleties
Public
IES retention analysis from PacBio CCS reads
bioinformatics genome-assembly genome-editing
bioinformatics genome-assembly genome-editing internal-eliminated-sequences
Python
•
MIT License
•2•5•13•0•Updated May 18, 2022May 18, 2022
gbtquick
Public
lazy person's blobtools2
Python
•
MIT License
•1•1•0•0•Updated Apr 21, 2022Apr 21, 2022
PORC
Public
Prediction Of Reassigned Codons
Python
•
GNU General Public License v3.0
•0•0•0•0•Updated Apr 14, 2022Apr 14, 2022
codetta
Public
Python
•
Other
•11•0•0•0•Updated Dec 17, 2021Dec 17, 2021
ParTIES
Public
PARamecium Toolbox for Interspersed DNA Elimination Studies
Perl
•
GNU General Public License v3.0
•4•0•0•0•Updated Aug 20, 2021Aug 20, 2021

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Swart lab

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All

32 repositories

mrub-intron-analysis

mrub-sorted-asm

loxodes-nucleosomes-workflow

mrub-sorted-compare

loxodes-bleties-workflow

DevPF_code

loxodes-assembly-workflow

pogigwasc-utils

eugene

trf_utils

loxodes-srna-workflow

loxodes-pogigwasc-workflow

loxodes-kmer-comp

loxodes-intronarrator-workflow

mnutils

ICOP_code

Intronarrator

pogigwasc

IES_nuc_density

hisat2

karyocode-analysis-busco

bleties-test-tthe

bleties-test-ptet

karyocode-analysis-porc

karyocode-workflow

bleties

gbtquick

PORC

codetta

ParTIES

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All

Repositories list

32 repositories