Nick Waters

Expert
@nickp60

Trying to figure those "bacteria" things that people keep talking about

fcid. Python

29

EzClermont. Phylotype your strains using Clermont's 2013 method: ezclermont.org

15

riboSeed. pipeline for using ribosomal flanking regions to improve bacterial genome assembly

9

sraFind. Get SRA accessions from nucleotide accessions, assuming the authors did the right thing and made the data available

8

happie. Horizontally Aquired Partial Pangenome of Inserted Elements

6

annofilt. Filter Prokka assemblies for pangenome analysis

4

cgfind. Minimal way to find and download complete prokaryotic genomes

3

ProphET. Perl

3

plentyofbugs. Find your sequenced isolate an compatable reference genome based on location, interests, and average nucleotide identity

2

open_utils. Python

1

SIS. a program to generate draft genome sequence scaffolds for prokaryotes

1

blobtools. Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets

1

rgi. Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.

1

pyutilsnrw. HTML

1
14
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