A collection of awesome things regarding all omics.

Exome/Capture/RNASeq Pipeline Implementation using snakemake

Computational Suite for Bioinformaticians and Biologists (CSBB) is a RShiny application developed with an intention to empower researchers from wet and dry lab to perform downstream Bioinformatics analysis

Project Manager for NGS data analysis

A bioinformatics best-practice analysis pipeline for calling structural variants (SVs), copy number variants (CNVs) and repeat region expansions (RREs) from short DNA reads

A set of CWL tools and workflows used by NCBI Computational Biology Branch for NGS data analysis

No description provided.

Pipelines for NGS data preprocessing by the Bock lab and friends

Reconstruction and analysis of viral and host genomes at multi-organ level

FASTQ-to-CodFreq pipeline for HIV-1 and SARS-CoV-2

A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data

A simple fastp-MultiQC nextflow pipeline

SARS-CoV-2 Genome Assembler

A fast, easy way to present complex bioinformatics pipelines to biologists

Mapping, filtering, and data hub visualisation pipeline for DNase, ATAC, ChIP data

Working example of snakemake tutorial using UAB Cheaha computing cluster via SLURM scheduler

command line and desktop tool for microbial variant calling

A flexible, automation and pragmatic workflow tool to process the NGS data.

scripts associated with yam genome assembly

Whole Exome Sequencing end-to-end pipeline. Starting from whole exome fastq files: Data QC, Adapter Trimming, Reference Genome Alignment, SAM/BAM Validation, Data Recalibration and Variant Calling.

Protein Analysis and Classifier Toolkit

Archived code for analyses in "Extensive phylogenomic discordance and the complex evolutionary history of the Neotropical cat genus Leopardus" (Lescroart et al. 2023, MBE)

Run Sentieon pipelines on Google Cloud Platform

High-performance Julia tool for sequence demultiplexing

:horse: CLinically Okay Metagenomic Pipeline :horse:

SOLIDA is command-line solution that facilitate the reproducibility and portability of NGS pipelines. It can easily organize the deployment, the data management and the execution of a Snakemake based workflow.

CSBB - Computational Suite For Bioinformaticians and Biologists

CB2-Experiments is the repository of scripts and data of experiments were performed to benchmark the performance of CB2.

BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data

DNAscan2 is a fast and efficient bioinformatics pipeline that allows for the analysis of DNA Next Generation sequencing data, requiring very little computational effort and memory usage