digenoma lab
The Di Genoma Lab is a research group that combine the development of new algorithms, genome analyses, and omic technologies to study complex biological systems
Chile
Pinned Repositories
.github
alignment-nf
Whole Exome/Whole Genome Sequencing alignment pipeline
bam2cram
A repository to convert BAM->CRAM files
biomining_metagenomes
Repository that holds data, scripts and figures regarding to Biomining MAGs-SMAG Profiling Article
fast-sg
Fast-SG: An alignment-free algorithm for ultrafast scaffolding graph construction from short or long reads.
k-count-nf
A nextflow pipeline to count k-mers and estimate genome size from WGS data
mag
Assembly and binning of metagenomes
somatic_point_mutations
call somatic point mutations from tumor/normal pairs
wengan
An accurate and ultra-fast hybrid genome assembler
wengan_demo
This repository contains a test dataset and the instructions to run Wengan (version 0.1).
digenoma lab's Repositories
digenoma-lab/.github
digenoma-lab/bam2cram
A repository to convert BAM->CRAM files
digenoma-lab/mag
Assembly and binning of metagenomes
digenoma-lab/alignment-nf
Whole Exome/Whole Genome Sequencing alignment pipeline
digenoma-lab/alnsl
Nextflow pipeline for short-read alignment
digenoma-lab/call_snv
A nextflow pipeline to call SNV from short-read sequences
digenoma-lab/fastqc-nf
digenoma-lab/hic-scaffolding-nf
Nextflow pipeline for scaffolding genome assemblies with Hi-C reads
digenoma-lab/k-count-nf
A nextflow pipeline to count k-mers and estimate genome size from WGS data
digenoma-lab/longreadstats
digenoma-lab/mutect-nf
Mutect pipeline with Nextflow
digenoma-lab/nextflow
A DSL for data-driven computational pipelines
digenoma-lab/nf-ngscheckmate
Nextflow workflow running NGScheckmate
digenoma-lab/prok-annotate
Annotation pipeline for prokaryotic genomes
digenoma-lab/purple-nf
Nextflow pipeline for CNV calling with PURPLE
digenoma-lab/somatic_point_mutations
call somatic point mutations from tumor/normal pairs
digenoma-lab/strelka2-nf
digenoma-lab/viralrecon
Assembly and intrahost/low-frequency variant calling for viral samples
digenoma-lab/wengan_demo
This repository contains a test dataset and the instructions to run Wengan (version 0.1).
digenoma-lab/assemblyStats
Run Assembly statistics on a genome assembly (BUSCO and assemblyStats and new_Assemblathon.pl)
digenoma-lab/bacannot
Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.
digenoma-lab/Germline-StructuralV-nf
Germline structural variant calling pipeline for short read WGS datasets
digenoma-lab/HBW
Hybrid Binning Wengan (HBW)
digenoma-lab/nf-bakta
A Nextflow pipeline for the annotation of bacterial genomes or MAGs running Bakta
digenoma-lab/nf-gene-fusions
A nextflow pipeline to call somatic gene fusions
digenoma-lab/nf-groot
A Nextflow pipeline for running Groot: a tool to type Antibiotic Resistance Genes (ARGs) in metagenomic samples.
digenoma-lab/nf-mag-depths
A nextflow pipeline to calculate depth of coverage from a metagenomic set of bins
digenoma-lab/oncovirus
prediction of somatic virus integration from WGS using hmftools
digenoma-lab/ppilon
Nextflow pipeline for polising a large genome using pilon
digenoma-lab/spg
Simple Pan-Genome workflow for MAGs