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IARC bioinformatics platform (@IARCbioinfo)

IARCbioinfo

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BAM-tricks

Tip and tricks for BAM files

R-tricks

Tip and tricks for R

awesome-TCGA

Curated list of TCGA resources

needlestack

Multi-sample somatic variant caller

IARC-nf

List of IARC bioinformatics nextflow pipelines

alignment-nf

Whole Exome/Whole Genome Sequencing alignment pipeline

RNAseq-nf

RNAseq analysis pipeline

VCF-tricks

Tip and tricks for VCF files

polysolver-singularity

Building a Singularity image of Polysolver

mutspec

Mutation Spectra Analysis

gatk4-GenotypeGVCFs-nf

Joint calling of gVCF, following GATK4 Best Practices

mutect-nf

Mutect pipeline with Nextflow

RNAseq_analysis_scripts

Scripts for RNA seq analysis

nextflow-course-2018

IARC nextflow course for pipeline users

medical_genomics_course

Material for medical genomics course

gatk4-HaplotypeCaller-nf

GATK4 HaplotypeCaller step, in gVCF mode, first step for subsequent whole cohort Joint Genotyping.

GDC-tricks

tricks to use the Genomics Data Commons portal from the National Cancer Institute

Gviz_multiAlignments

R script for multiple BAM alignments viewing using Gviz (bioconductor package)

SBG-CGC_course2018

IARC course on analyzing TCGA data in the SevenBridges Genomics CancerGenomicsCloud (SBG-CGC)

table_annovar-nf

annotation of variants with annovar and nextflow

template-nf

Empty template for nextflow pipelines

strelka2-nf

GVCF_pipeline-nf

Nextflow pipeline for generate GVCF from BAM with GenomeAnalysisTK with step of realignment

abra-nf

Nextflow pipeline for ABRA (Assembly Based ReAligner)

integration_analysis_scripts

Scripts for multi-omics integration

GATK-Alignment-nf

Perform bwa alignment and pre-processing following GATK best practices

purple-nf

Nextflow pipeline for CNV calling with PURPLE

Imputation-nf

Imputation pipeline

gatk4-DataPreProcessing-nf

Nextflow pipeline for pre-process BAM(s) with hg38 and GATK4

conpair-nf

Nextflow pipeline for Conpair (concordance and contamination estimator)

MESOMICS_data

Data and scripts associated with MESOMICS paper and data note

addreplacerg-nf

Apply samtools addreplacerg to add a new read group and assign all reads to it in a BAM file

methylkey

facets-nf

Pipeline using facets for fraction and copy number estimate from tumor/normal sequencing

nextflow-hackathon-2017

ampliconarchitect-nf

Nextflow pipeline to discover ecDNA on cancer genomes

ITH_pipeline

Pipeline to study intra tumor heterogeneity using HATCHet, DeCiFer and ClonEvol

strelka-nf

EGA-tricks

tricks to use the European Genome-Phenome Archive from the European Bioinformatics Institute

CODEX-nf

Pipeline for copy number variant calling from Whole Exome sequencing data using CODEX

NGSCheckMate-nf

Nextflow pipeline to detect matched BAMs with NGSCheckMate

fastqc-nf

RF-mut-f

A random forest implementation to filter germline mutations of tumor-only samples

LiftOver-nf

Convert BED/VCF files between two genomes with nextflow

EPIDRIVER2020

Scripts writen for EPIDERIVER project

bamsurgeon-nf

bamsurgeon with step of variant simulation encapsulated with nextflow

qualimap-nf

intro-cancer-genomics

Introduction to cancer genomics

LSF-tricks

Tip and tricks for IBM platform LSF HPC job scheduler

Methylation_analysis_scripts

R scripts for Illumina array analyses

scanMyWorkDir

Non-destructive & Informative scan of a NextFlow work folder

gene-fusions-nf

A nextflow pipeline to call somatic gene fusions

wsearch-nf

Microbiome analysis with usearch, vsearch and phyloseq

bam_realignment-nf

bam realignment with samtools, bwa and sambamba

bametrics-nf

Nextflow pipeline to compute average metrics from reads that overlap a given set of positions

ssvht

A set of scripts to call somatic structural variants

mpileup-nf

Nextflow pipeline for coverage computation with samtools mpileup (bed parallelization)

snpeff_annotation-nf

Annotate VCF files with SnpEff and dbSnp

PVAmpliconFinder

IARC-SLC-meetings

IARC Synergie Lyon Cancer bioinformatics meetings reports

marathon-wgs

A pipeline to study intratumor heterogeneity (ITH) with Canopy

SpatialPCAForWSIs

HaloAE

Unsupervised anomaly detection model using a Halonet auto-encoder.

PRSice-nf

Pipeline to compute polygenic risk scores

data_test

Small data files to test IARC nextflow pipelines