rrwick/Perfect-bacterial-genome-tutorial

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rrwick/Perfect-bacterial-genome-tutorial

rrwick

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This repo contains a tutorial for assembling a bacterial genome to perfection using short and long reads.

Head over to this repo's wiki for the tutorial and all supporting content.

Bandage

a Bioinformatics Application for Navigating De novo Assembly Graphs Easily

Unicycler

hybrid assembly pipeline for bacterial genomes

Porechop

adapter trimmer for Oxford Nanopore reads

Basecalling-comparison

A comparison of different Oxford Nanopore basecallers

Trycycler

A tool for generating consensus long-read assemblies for bacterial genomes

Filtlong

quality filtering tool for long reads

Long-read-assembler-comparison

Benchmarking of long-read assembly tools for bacterial whole genomes

Badread

a long read simulator that can imitate many types of read problems

Polypolish

a short-read polishing tool for long-read assemblies

Deepbinner

a signal-level demultiplexer for Oxford Nanopore reads

Metagenomics-Index-Correction

Bacsort

a collection of scripts for organising bacterial genomes by species

Minipolish

A tool for Racon polishing of miniasm assemblies

Assembly-Dereplicator

A tool for removing redundant genomes from a set of assemblies

August-2019-consensus-accuracy-update

A short analysis of Oxford Nanopore consensus accuracy for bacterial genome assemblies

Verticall

Recombination-free trees

Rebaler

reference-based long read assemblies of bacterial genomes

MinION-desktop

Scripts and programs for the Holt Lab's MinION desktop

Bacterial-genome-assemblies-with-multiplex-MinION-sequencing

Core-SNP-filter

a tool to filter sites in a FASTA-format whole-genome pseudo-alignment

Fast5-to-Fastq

A simple tool for extracting reads from Oxford Nanopore fast5 files

Compare-annotations

A script for comparing old vs new versions of genome annotations

LinesOfCodeCounter

A Python script to count lines of code in a directory for specific file extension, excluding blank/comment lines

Catpac

a Contig Alignment Tool for Pairwise Assembly Comparison

Small-plasmid-Nanopore

DASCRUBBER-wrapper

Wrapper script for easier read scrubbing with DASCRUBBER

GFA-dead-end-counter

a tool for counting dead ends in GFA assembly graphs

SPAdes-Contig-Graph

a tool for creating a FASTG contig graph from a SPAdes assembly

Langtons-Ant-Animator

Program for creating Langton's Ant animations

Klebsiella-assembly-species

a tool for assigning species to Klebsiella assemblies

Circular-Contig-Extractor

ONT-assembler-benchmark

KleborateModular

A modular rewrite of Kleborate

SRST2-table-from-assemblies

This is a tool for conducting a gene screen on assemblies, producing an SRST2-like output.

IDBA-to-GFA

Grovolve

Demonstration of evolution by natural selection

Trycycler-paper

Supplementary figures, tables and scripts for the Trycycler paper

Nanopore-barcode-binner

Nanopore-read-processor

A script for sorting, assessing and converting Oxford Nanopore reads

Adapter-assembler

Bugraft

Demonstration of speciation and descent from a common ancestor

Unicycler-assembly-tests

MLST-from-SRST2

This tool uses a table of compiled results from SRST2 to create an MLST-like scheme.

SPAdes-completion-checker

Tool to assess SPAdes assembly graph paths using read depth

Irsat

Iterative Read Subset Assembly Tool

Polypolish-paper

Supplementary figures, tables and scripts for the Polypolish paper

rrwick.github.io