MaestSi/Illumina_variant_calling

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Created over 3 years ago
Updated almost 2 years ago

MaestSi/Illumina_variant_calling

MaestSi

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A quality check, alignment and small variant calling pipeline for Illumina paired-end reads

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A Meta-barcoding pipeline for analysing ONT data in QIIME2 framework

ONTrack

A MinION-based pipeline for tracking species biodiversity

MetaBlast

A Metagenomic pipeline for parallel Blast analysis and report generation.

CharONT2

A NextFlow ONT-based pipeline for characterizing long genomic regions

ONTrack2

A Nextflow MinION-based pipeline for tracking species biodiversity

nf-m6anet

A NextFlow pipeline for m6A detection from Nanopore direct RNA-seq data

CharONT

An ONT-based pipeline for characterizing long genomic regions

MetaKraken2

A Metagenomic pipeline for Kraken2 analysis and Krona report generation.

UMInator

A Nextflow pipeline for generating consensus sequences from Nanopore reads tagged with UMIs

ONT_preprocessing

A preprocessing pipeline for ONT data

pycoMethFlow

A nextflow pipeline for running pycoMeth

QIIME2_Illumina

A Meta-barcoding pipeline for analysing Illumina data in QIIME2 framework

ONToHap

An ONT-based pipeline for haplotype phasing

Bionano_fixdups

A script for removing artificial duplications introduced by Bionano solve scaffolding pipeline

Covid19_ONT_Artic

A set of scripts for running the ARTIC pipeline from fast5 ONT data to filtered SARS-CoV-2 variants and coverage plots

nf-msspe

A NextFlow pipeline for Metagenomic Sequencing with Spiked Primer Enrichment

MosaicViewer_FMR1

A pipeline for schematic IGV visualization of FMR1 alleles with somatic mosaicism

nf-eligos

A NextFlow pipeline for modifications detection from Nanopore direct RNA-seq data

MosaicViewer_HTT

A pipeline for schematic IGV visualization of HTT alleles with somatic mosaicism

MosaicViewer_CNBP

A pipeline for schematic IGV visualization of expanded CNBP alleles with somatic mosaicism