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abra-nf

Nextflow pipeline for ABRA (Assembly Based ReAligner)

acnviewer-singularity

Singularity version of acnviewer

addreplacerg-nf

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

aiml-wg

Repository with scripts from IARC's Machine Learning / Artificial Intelligence working group

alignment-nf

Whole Exome/Whole Genome Sequencing alignment pipeline

ampliconarchitect

AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates the architecture of the amplicon. In the current version, AA takes as input next generation sequencing reads (paired-end Illumina reads) mapped to the hg19/GRCh37 reference sequence and one or more regions of interest. Please "watch" this repository for improvements in runtime, accuracy and annotations for GRCh38 human reference genome coming up soon.

ampliconarchitect-nf

Nextflow pipeline to discover ecDNA on cancer genomes

amptools

Tools for dealing with amplicon experiments

awesome-cancerevolution

awesome-clonality

A curated list of awesome clonality and tumor heterogeneity resources

awesome-tcga

Curated list of TCGA resources

bam-tricks

Tip and tricks for BAM files

bam2cram-nf

A repository to convert BAM->CRAM files

bam2peaks-nf

Nextflow pipeline for peaks calling with MACS

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

bamsurgeon-nf

bamsurgeon with step of variant simulation encapsulated with nextflow

bqsr-nf

Nextflow script for base quality score recalibration of bam files using GATK

codex-nf

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

conpair-nf

Nextflow pipeline for Conpair (concordance and contamination estimator)

damage-estimator-nf

Nextflow pipeline to run "Damage Estimator"

data_test

Small data files to test IARC nextflow pipelines

dpclust-nf

Nextflow workflow to run DPclust on a series of samples

draftpolisher

A tool for the polishing of draft sequences

drmetrics

ega-tricks

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

epidriver2020

Scripts writen for EPIDERIVER project

esmoopen_lungnenomicscohort

facets-nf

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

fasta-tricks