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bacterial-genomics-tutorial

beavr

BEAVR: A Browser-based tool for the Exploration And Visualization of RNAseq data

canu

A single molecule sequence assembler for genomes large and small.

dotplotly

Generate an interactive dot plot from mummer or minimap alignments

fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

fastq-dl

Download FASTQ files from SRA or ENA repositories.

genomad

geNomad: Identification of mobile genetic elements

genotype_plot

A set of functions to visualise genotypes based on a VCF

isescan_stats

Condense and summarize many results form ISEScan into CSV for heatmaps

mgems

mGEMS Genomic epidemiology with mixed samples

mitocode_r_workshops

R markdown files which I have prepared for my work buddies at Ochota Campus in Warsaw,Poland as materials for the workshops aiming at teaching biologist the benefits of using R for data analysis

nanopolish

Signal-level algorithms for MinION data

nasqar

NASQAR: A web-based platform for High-throughput sequencing data analysis and visualization

ngspeciesid

Reference-free clustering and consensus forming of long-read amplicon sequencing

ntedit

✏️ultra fast and scalable genome assembly polishing

pipits

Automated pipeline for analyses of fungal ITS from the Illumina

ragtag

Tools for fast and flexible genome assembly scaffolding and improvement

sniffles

Structural variation caller using third generation sequencing

snippy

:scissors: :zap: Rapid haploid variant calling and core genome alignment

tormes

Making whole bacterial genome sequencing data analysis easy

unicycler

hybrid assembly pipeline for bacterial genomes

unimap

A fork of minimap2 optimized for assembly-to-reference alignment

useful-scripts

utility

Useful bash one-liners for bioinformatics.