ayoraind Goto Github PK

abricate

:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes

another_test

ariba

Antimicrobial Resistance Identification By Assembly

assembly

Git cloned assembly pipeline for short reads

ayoraind.github.io

Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

bacass

Simple bacterial assembly and annotation pipeline

bactmap

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

bash_snippets

bracken

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

christmas-2021

cramino

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

day_1_exercise

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

genomic_environment

From assembly and reference gene, extracts the contig containing the reference gene and annotates the possible genomic environment

hdna_removal_and_mapping_stats

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

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

hello-world

Just another repository

homework-o

R_Tutorial_first_Repo

kraken

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

kraken2

Nextflow pipeline implementing kraken2 for taxonomic assignment

krocus

Nextflow pipeline for MLST from uncorrected long reads

mlst

nextflow pipeline for mlst where schemes can be forced optionally.

nanolyse

Modified nextflow pipeline to filter out unwanted genomes

nanoplot

modified nextflow pipeline to generate Nanoplot and combined Nanostats output

nanoqc

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

nf-training

Learning how to use the workflow called nextflow