Ryan Wick

Bandage. a Bioinformatics Application for Navigating De novo Assembly Graphs Easily

Unicycler. hybrid assembly pipeline for bacterial genomes

Filtlong. quality filtering tool for long reads

Porechop. adapter trimmer for Oxford Nanopore reads

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

Basecalling-comparison. A comparison of different Oxford Nanopore basecallers

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

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

Polypolish. a short-read polishing tool for long-read assemblies

Long-read-assembler-comparison. Benchmarking of long-read assembly tools for bacterial whole genomes

Perfect-bacterial-genome-tutorial. Python

Deepbinner. a signal-level demultiplexer for Oxford Nanopore reads

Metagenomics-Index-Correction. Python

Assembly-Dereplicator. A tool for removing redundant genomes from a set of assemblies

Minipolish. A tool for Racon polishing of miniasm assemblies

Bacsort. a collection of scripts for organising bacterial genomes by species

Verticall. Recombination-free trees

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

August-2019-consensus-accuracy-update. A short analysis of Oxford Nanopore consensus accuracy for bacterial genome assemblies

Rebaler. reference-based long read assemblies of bacterial genomes

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

MinION-desktop. Scripts and programs for the Holt Lab's MinION desktop

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

condaenvlist. a simple tool for listing conda environments with descriptions

Circular-Contig-Extractor. Python

Small-plasmid-Nanopore. Python

Catpac. a Contig Alignment Tool for Pairwise Assembly Comparison

Langtons-Ant-Animator. Program for creating Langton's Ant animations

Klebsiella-assembly-species. a tool for assigning species to Klebsiella assemblies

DASCRUBBER-wrapper. Wrapper script for easier read scrubbing with DASCRUBBER

Are-reads-required. Python

SPAdes-Contig-Graph. a tool for creating a FASTG contig graph from a SPAdes assembly

Assembly-topology. Assembly topology from long-read alignments

GFA-dead-end-counter. a tool for counting dead ends in GFA assembly graphs

ONT-assembler-benchmark. Python

Grovolve. Demonstration of evolution by natural selection

Trycycler-paper. Supplementary figures, tables and scripts for the Trycycler paper

Nanopore-barcode-binner. C++

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

IDBA-to-GFA. Python

Nanopore-read-processor. A script for sorting, assessing and converting Oxford Nanopore reads

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

Irsat. Iterative Read Subset Assembly Tool

SPAdes-completion-checker. Tool to assess SPAdes assembly graph paths using read depth