Discover rrwick/Rebaler Open Source project by Ryan Wick (@rrwick)

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Rank 604,252 (Top 12 %)
Language
Python
License
GNU General Publi...
Created about 7 years ago
Updated over 3 years ago

rrwick

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reference-based long read assemblies of bacterial genomes

Bandage

a Bioinformatics Application for Navigating De novo Assembly Graphs Easily

C++

582

Unicycler

hybrid assembly pipeline for bacterial genomes

C++

559

Porechop

adapter trimmer for Oxford Nanopore reads

C++

337

Basecalling-comparison

A comparison of different Oxford Nanopore basecallers

Python

313

Trycycler

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

Python

306

Filtlong

quality filtering tool for long reads

C++

285

Long-read-assembler-comparison

Benchmarking of long-read assembly tools for bacterial whole genomes

Python

170

Badread

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

Python

168

Polypolish

a short-read polishing tool for long-read assemblies

Rust

143

Deepbinner

a signal-level demultiplexer for Oxford Nanopore reads

Python

124

Perfect-bacterial-genome-tutorial

Python

118

Metagenomics-Index-Correction

Python

Bacsort

a collection of scripts for organising bacterial genomes by species

Python

Minipolish

A tool for Racon polishing of miniasm assemblies

Python

Assembly-Dereplicator

A tool for removing redundant genomes from a set of assemblies

Python

August-2019-consensus-accuracy-update

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

Python

Verticall

Recombination-free trees

Python

MinION-desktop

Scripts and programs for the Holt Lab's MinION desktop

Python

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

Shell

Core-SNP-filter

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

Rust

Fast5-to-Fastq

A simple tool for extracting reads from Oxford Nanopore fast5 files

Python

Compare-annotations

A script for comparing old vs new versions of genome annotations

Python

LinesOfCodeCounter

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

Python

Catpac

a Contig Alignment Tool for Pairwise Assembly Comparison

Python

Small-plasmid-Nanopore

Python

DASCRUBBER-wrapper

Wrapper script for easier read scrubbing with DASCRUBBER

Python

GFA-dead-end-counter

a tool for counting dead ends in GFA assembly graphs

Rust

SPAdes-Contig-Graph

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

Python

Langtons-Ant-Animator

Program for creating Langton's Ant animations

C++

Klebsiella-assembly-species

a tool for assigning species to Klebsiella assemblies

Python

Circular-Contig-Extractor

Python

ONT-assembler-benchmark

Python

KleborateModular

A modular rewrite of Kleborate

Python

SRST2-table-from-assemblies

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

Python

IDBA-to-GFA

Python

Grovolve

Demonstration of evolution by natural selection

C++

Trycycler-paper

Supplementary figures, tables and scripts for the Trycycler paper

Python

Nanopore-barcode-binner

C++

Nanopore-read-processor

A script for sorting, assessing and converting Oxford Nanopore reads

Python

Adapter-assembler

C++

Bugraft

Demonstration of speciation and descent from a common ancestor

C++

Unicycler-assembly-tests

Shell

MLST-from-SRST2

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

Python

SPAdes-completion-checker

Tool to assess SPAdes assembly graph paths using read depth

Python

Irsat

Iterative Read Subset Assembly Tool

Python

Polypolish-paper

Supplementary figures, tables and scripts for the Polypolish paper

Python

rrwick.github.io

SCSS

rrwick/Rebaler

rrwick

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