ayoraind

ONT-Pipeline

A Nextflow Assembly Pipeline for Downstream Analysis of long reads (ONT) - Genome Assembly .

hDNA_removal_and_mapping_stats

A pipeline to remove human DNA from long-read metagenomes and extract microbial reads.

kraken2

Nextflow pipeline implementing kraken2 for taxonomic assignment

Nanoplot

modified nextflow pipeline to generate Nanoplot and combined Nanostats output

strainberry

Nextflow Pipeline for Strain Resolution from Long Reads

assembly

Git cloned assembly pipeline for short reads

bactmap

A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

bracken

Nextflow pipeline implementing Bracken. It uses the conda container where necessary.

kraken

Nextflow pipeline implementing Kraken. It uses the conda container where necessary.

krocus

Nextflow pipeline for MLST from uncorrected long reads

bacass

Simple bacterial assembly and annotation pipeline

bash_snippets

cramino

nextflow pipeline to assess bam/cram files (suitable for long read sequence data).

error-correction

A Nextflow Pipeline using tools hosted in conda containers to correct errors in long-read assemblies

fastqc

Adaptable nextflow pre-assembly QC pipeline

flye

Nextflow pipeline that utilizes the Flye Assembler

genome-annotation-and-pangenome-analysis

A nextflow pipeline to annotate bacterial genomes and generate a pangenome

genome_annotation

Nextflow pipeline to annotate genomes using prokka or bakta

hDNA_removal_and_mapping_statsv2

differ from hDNA_removal_and_mapping_stats in the option to specify the number of times reads are mapped to the human genome

mlst

nextflow pipeline for mlst where schemes can be forced optionally.

Nanolyse

Modified nextflow pipeline to filter out unwanted genomes

nanoQC

Nextflow pre-assembly QC pipeline for reads generated using the Oxford Nanopore Technology platform

nxf_plassembler

plasmidfinder

Nextflow pipeline utilizing plasmidfinder for in silico Inc Typing

python_snippets

Snippets for parsing files generated from the bioinformatic analysis of sequence data.

quast

Nextflow pipeline to generate post-assembly summary QC file

SKA

Nextflow pipeline utilizing the ska fastq, ska align, ska merge, and ska distance commands

strainberry-accessories

Works on generating relevant assembly statistics report from strainberry assemblies (or any assembly with a corresponding reference)

strainyMAG

A nextflow pipeline version of the original strainyMAG

tracm_nextflow

Nextflow pipeline incorporating the tracm alignment step alone.