GENome EXogenous (GENEX) sequence detection

This is a computational workflow for detecting coordinates of microbial-like or human-like sequences in eukaryotic and procaryotic reference genomes. The workflow accepts a reference genome in FASTA-format and outputs coordinates of microbial-like (human-like) regions in BED-format. The workflow builds a Bowtie2 index of the reference genome and aligns pre-computed microbial (GTDB v.214 or NCBI RefSeq release 213) or human (hg38) pseudo-reads to the ...

Overview

Developmental version of MSC: This github page contains developmental version of R package for Multi-scale clustering (MSC) to perform single-cell transcriptome clustering. The manuscript is currently under review.

Installation:

MEGENA needs to be installed, prior to MSC installation: library(devtools); install_github("songw01/MEGENA");

For installation for developmental github version: library(devtools); install_github("songlabcodes/MSC");

Vignettes [PBMC 8k ...

MRanalysis is an interactive R Shiny application designed for Mendelian randomization analysis.

MRanalysis

Mendelian randomization (MR) has emerged as a powerful epidemiological method for inferring causal relationships between exposures and outcomes using genome-wide association study (GWAS) summary data. By leveraging instrumental variables (IVs), such as single nucleotide polymorphisms (SNPs), MR can revolutionize our understanding of disease etiology, ...

Imputation Workflow h3abionet/chipimputation

Introduction

Imputation is likely to be run ...

VIsoQLR: an interactive tool for the detection, quantification and fine-tuning of isoforms using long-read sequencing

VIsoQLR is an interactive analyzer, viewer and editor for the semi-automated identification and quantification of known and novel isoforms using long-read sequencing data. VIsoQLR is tailored to thoroughly analyze mRNA expression and maturation in low-throughput splicing assays. This tool takes sequences aligned to a reference, defines consensus splice sites, and quantifies ...

Workflow for long read quality control, contamination filtering, assembly, variant calling and annotation.

Steps:

• Preprocessing of reference file : https://workflowhub.eu/workflows/1818
• LongReadSum before and after filtering (read quality control)
• Filtlong filter on quality and length
• Flye assembly
• Minimap2 mapping of reads and assembly
• Clair3 variant calling of reads
• Freebayes variant calling of assembly
• Optional Bakta annotation of genomes with no reference
• SnpEff building ...

**Workflow for preprocessing a reference file. **

Steps: -When a GenBank file is not provided, it is downloaded from NCBI based on a accession number. -When multiple plasmid GenBank files are provided, they are merged into one file. -When any amount of plasmid GenBank files are provided, the reference is merged with the plasmid GenBank file(s) into one file. A FASTA file is also extracted. -When no plasmid Genbank files are provided, a FASTA file is extracted from the reference GenBank file. -A ...

PriorR

Priorr is a prioritization program of disease-linked genetic variants devoloped within the Genetics&Genomics Department of La Fundacion Jimenez Diaz University Hospital. Priorr is conceived to analyse the output of the FJD-pipeline of SNVs or CNVs. This software program offers a number of useful functionalities for variant analysis such as: filtering by a virtual panel of genes. manual control of different population frequencies or pathogenicity predictors or filtering out variants ...

GLOWgenes

Prioritization of gene diseases candidates by disease-aware evaluation of heterogeneous evidence networks Visit www.glowgenes.org for more information

Citing

de la Fuente L, Del Pozo-Valero M, Perea-Romero I, Blanco-Kelly F, Fernández-Caballero L, Cortón M, Ayuso C, Mínguez P. Prioritization of New Candidate Genes for Rare Genetic Diseases by a Disease-Aware Evaluation of Heterogeneous Molecular Networks. International Journal of Molecular Sciences. 2023; 24(2):1661. ...

WHALE: (W)orkflow for (H)uman-genome (A)nalysis of (L)ong-read (E)xperiments

Introduction

WHALE is a bioinformatics pipeline based on Nextflow and nf-core for long-read DNA sequencing analysis. It takes a samplesheet as input and performs quality control, alignment, variant calling and annotation.

Pipeline summary

1. Read QC (FastQC)
2. Present QC for raw reads (MultiQC)
3. Alignment ...