ayoraind
Post-doctoral Scientist (Microbiologist/Bioinformatician/data scientist) at the Institute for Infection Prevention and Hospital Epidemiology, Freiburg, Germany.
Universitätsklinikum FreiburgGermany
Pinned Repositories
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
bactmap
A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
hDNA_removal_and_mapping_stats
A pipeline to remove human DNA from long-read metagenomes and extract microbial reads.
krocus
Nextflow pipeline for MLST from uncorrected long reads
Nanoplot
modified nextflow pipeline to generate Nanoplot and combined Nanostats output
ONT-Pipeline
A Nextflow Assembly Pipeline for Downstream Analysis of long reads (ONT) - Genome Assembly .
strainberry
Nextflow Pipeline for Strain Resolution from Long Reads
ayoraind's Repositories
ayoraind/ONT-Pipeline
A Nextflow Assembly Pipeline for Downstream Analysis of long reads (ONT) - Genome Assembly .
ayoraind/hDNA_removal_and_mapping_stats
A pipeline to remove human DNA from long-read metagenomes and extract microbial reads.
ayoraind/kraken2
Nextflow pipeline implementing kraken2 for taxonomic assignment
ayoraind/Nanoplot
modified nextflow pipeline to generate Nanoplot and combined Nanostats output
ayoraind/strainberry
Nextflow Pipeline for Strain Resolution from Long Reads
ayoraind/bactmap
A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
ayoraind/bracken
Nextflow pipeline implementing Bracken. It uses the conda container where necessary.
ayoraind/kraken
Nextflow pipeline implementing Kraken. It uses the conda container where necessary.
ayoraind/krocus
Nextflow pipeline for MLST from uncorrected long reads
ayoraind/bacass
Simple bacterial assembly and annotation pipeline
ayoraind/bash_snippets
ayoraind/cramino
nextflow pipeline to assess bam/cram files (suitable for long read sequence data).
ayoraind/error-correction
A Nextflow Pipeline using tools hosted in conda containers to correct errors in long-read assemblies
ayoraind/fastqc
Adaptable nextflow pre-assembly QC pipeline
ayoraind/flye
Nextflow pipeline that utilizes the Flye Assembler
ayoraind/genome-annotation-and-pangenome-analysis
A nextflow pipeline to annotate bacterial genomes and generate a pangenome
ayoraind/genome_annotation
Nextflow pipeline to annotate genomes using prokka or bakta
ayoraind/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
ayoraind/mlst
nextflow pipeline for mlst where schemes can be forced optionally.
ayoraind/Nanolyse
Modified nextflow pipeline to filter out unwanted genomes
ayoraind/nanoQC
Nextflow pre-assembly QC pipeline for reads generated using the Oxford Nanopore Technology platform
ayoraind/nxf_plassembler
ayoraind/ONT_adapter_removal_and_read_filtration
ayoraind/plasmidfinder
Nextflow pipeline utilizing plasmidfinder for in silico Inc Typing
ayoraind/python_snippets
Snippets for parsing files generated from the bioinformatic analysis of sequence data.
ayoraind/quast
Nextflow pipeline to generate post-assembly summary QC file
ayoraind/SKA
Nextflow pipeline utilizing the ska fastq, ska align, ska merge, and ska distance commands
ayoraind/strainberry-accessories
Works on generating relevant assembly statistics report from strainberry assemblies (or any assembly with a corresponding reference)
ayoraind/strainyMAG
A nextflow pipeline version of the original strainyMAG
ayoraind/tracm_nextflow
Nextflow pipeline incorporating the tracm/tracs alignment step alone.