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itrap
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Improved T-cell Receptor Antigen Pairing
public

public

This repository contains the code to identify ITRAP filters for single-cell immune profiling data. ITRAP is developed by Mort...
Pandas Snakemake ggplot2 matplotlib numpy PyYAML scipy seaborn
Free
10
metagem
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:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
public

public

Note An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic inte...
JSON raw sequence reads Genome assembly Quality control report prodigal MEGAHIT BWA CheckM fastp kallisto MaxBin memote MetaBAT 2 metaprokka MetaWRAP Quant Roary SAMtools Snakemake SqueezeMeta CONCOCT carve gtdbtk smetana metagenomics
Free
35
workflow-coastal-hydrowaq
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Porting and deploying the HiSea use case on C-SCALE
public

public

C-SCALE workflow solutions are intended to give users a template and reusable components to start building monitoring, modell...
CLICK Pandas Snakemake Delft3D
Free
16
pacbio_snakemake
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A Snakemake pipeline to go from raw .subreads.bam PacBio Iso-Seq to assembled mRNA isoforms (FASTA format)
public

public

A Snakemake workflow for processing PacBio raw subreads.bam into polished mRNA isoforms in FASTA format. Optionnally, lon...
gffread IsoSeq3 MLM pbmm2 SAMtools Snakemake
Free
9
sv-jim
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SV calling using multiple software tools with results evaluated using the Jaccard Index Measure
public

public

Multi-stage Snakemake pipeline that combines python and BASH scripts for Structural Variant (SV) calling with multiple third-...
sniffles svim tabix BCFtools Minimap2 SAMtools Snakemake cuteSV
Free
457
molecular-dynamics-simulation
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HPC Molecular Dynamics Simulation Workflow: CWL Version of md_list.py
public

public

This repository is part of a series of repositories mirroring the workflow and launchers in https://github.com/bioexcel/biob...
Molecular simulation data CWL biobb_gromacs genion Gromacs editconf Molecular dynamics
Free
7

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