genomicsiter Goto Github PK

isafe

Pinpoints the mutation favored by selection

ismc

The integrated Sequentially Markovian Coalescent

megaqc

Web application to collect and visualise data across multiple MultiQC runs.

miseq_wetlab_sop

mitogenomes

mixemt

A tool for phylogenetic interpretation of human mtDNA sequence mixtures

monkeypox

Monkeypox public repository

mosdepth

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

mutational-burden-and-ccrcc-mortality

Repository with the whole code of our pipeline used in the analysis of mortality in metastatic clear cell kidney cancer carcinoma

nanoclust

NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads

nanodj

NanoDJ: A Dockerized Jupyter Notebook for Interactive Oxford Nanopore MinION Sequence Manipulation and Genome Assembly

nanortax

Real-time analysis pipeline for nanopore 16S rRNA data

nextflow

nf-gatk_exome_preprocess

Adapted from the GATK best practice guide to preprocess whole exome sequencing (WES) data

ngi-exoseq

(WIP) Nextflow Exome Sequencing Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure. https://ngisweden.scilifelab.se/

ngi-methylseq

Methylation (Bisulfite-Sequencing) Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

ngi-rnaseq

Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

ngsrelate

one-liners

Frequently used commands in Bioinformatics

opentda

Open source Python library for topological data analysis (TDA)

pcodebooks

Persistence BOW

ped

Polymorphic Edge Detection - An efficient polymorphism detector for NGS data

pfgenetics

Collaborative genetic studies of idiopathic pulmonary fibrosis

ph_datasets

Persistent Homology Datasets

picardmetrics

:vertical_traffic_light: Run Picard on BAM files and collate 90 metrics into one file.

pipeline-builder

Pipeline Builder is a JavaScript library for visualizing and constructing bioinformatics workflows, using Workflow Description Language (WDL)

pipeline-resources

Bioinformatics Pipeline and Visualization resources

piper

A genomics pipeline build on top of the GATK Queue framework. Main repository: https://github.com/NationalGenomicsInfrastructure/piper (make sure you fork from there)

popstats

Population genetic summary statistics

precisionfda_nctr-indel-calling-oncopanel-sequencing-data-challenge