GSC (Genotype Sparse Compression)

Genotype Sparse Compression (GSC) is an advanced tool for lossless compression of VCF files, designed to efficiently store and manage VCF files in a compressed format. It accepts VCF/BCF files as input and utilizes advanced compression techniques to significantly reduce storage requirements while ensuring fast query capabilities. In our study, we successfully compressed the VCF files from the 1000 Genomes Project (1000Gpip3), consisting of 2504 samples and 80 ...

GSC (Genotype Sparse Compression)

Genotype Sparse Compression (GSC) is an advanced tool for lossless compression of VCF files, designed to efficiently store and manage VCF files in a compressed format. It accepts VCF/BCF files as input and utilizes advanced compression techniques to significantly reduce storage requirements while ensuring fast query capabilities. In our study, we successfully compressed the VCF files from the 1000 Genomes Project (1000Gpip3), consisting of 2504 samples and 80 ...

This is the workflow for the biodiversity component of the cultural ecosystems digital twin

This is the workflow for the recreation potential component of the cultural ecosystems digital twin

GBMatch_CNN

Work in progress... Predicting TS & risk from glioblastoma whole slide images

Reference

Upcoming paper: stay tuned...

Dependencies

python 3.7.7

randaugment by Khrystyna Faryna: https://github.com/tovaroe/pathology-he-auto-augment

tensorflow 2.1.0

scikit-survival 0.13.1

pandas 1.0.3

lifelines 0.25.0

Description

The pipeline implemented here predicts transcriptional subtypes and survival of glioblastoma patients based on H&E stained whole slide scans. Sample data is ...

A hecatomb is a great sacrifice or an extensive loss. Heactomb the software empowers an analyst to make data driven decisions to 'sacrifice' false-positive viral reads from metagenomes to enrich for true-positive viral reads. This process frequently results in a great loss of suspected viral sequences / contigs.

For information about installation, usage, tutorial etc please refer to the documentation: https://hecatomb.readthedocs.io/en/latest/

Quick start guide

Install Hecatomb from Bioconda ...

beacon-omop-worker-workflows

Purge Duplicate Contigs

Purge contigs marked as duplicates by purge_dups in a single haplotype(could be haplotypic duplication or overlap duplication) This workflow is the 6th workflow of the VGP pipeline. It is meant to be run after one of the contigging steps (Workflow 3, 4, or 5)

Inputs

1. Genomescope model parameters [txt] (Generated by the k-mer profiling workflow)
2. Hifi long reads - trimmed [fastq] (Generated by Cutadapt in the contigging workflow)
3. Assembly to purge (e.g. hap1) ...

This is part of a series of workflows to annotate a genome, tagged with TSI-annotation. These workflows are based on command-line code by Luke Silver, converted into Galaxy Australia workflows.

The workflows can be run in this order:

• Repeat masking
• RNAseq QC and read trimming
• Find transcripts
• Combine transcripts
• Extract transcripts
• Convert formats
• Fgenesh annotation

About this workflow:

• Inputs: transdecoder-peptides.fasta, transdecoder-nucleotides.fasta
• Runs many steps ...

This is part of a series of workflows to annotate a genome, tagged with TSI-annotation. These workflows are based on command-line code by Luke Silver, converted into Galaxy Australia workflows.

The workflows can be run in this order:

• Repeat masking
• RNAseq QC and read trimming
• Find transcripts
• Combine transcripts
• Extract transcripts
• Convert formats
• Fgenesh annotation

About this workflow:

• Input: merged_transcriptomes.fasta.
• Runs TransDecoder to produce longest_transcripts.fasta ...