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assembly-stats

Provides some of the common assembly statistics used to identify how good a metagenomic assembly is.

bio-py

Some useful python scripts for biologists

consort

Consort: amplicon sequence variant based analysis of 16S rRNA datasets from minimal consortia

consortm

ConsortM: MALDI-based consortia monitoring

convert-text-to-hyperlinks

This script searches for hyperlink text in the layout, and converts it to QuarkXPress hyperlinks

csv-to-html-table

curver

dna2proteins

This is an adaptation of https://github.com/prestevez/dna2proteins which outputs all protein sequences instead of the best one. I take no credit for writing the code or responsibility if it doesnt work.

extractinator

Uses GFF files to identify regions of interest within a sequence file and produce a separate file of only these extracted regions.

gan

📜 the Great Automatic Nomenclator — The Next Million Names for Archaea and Bacteria

gmms

A manually curated database of human gut metabolic modules.

gutlipases

Annotation of the microbial lipases within the mammalian gut

imgmc

Repository of the integrated mouse gut metagenomic catalog

investigut

ivon

Integrative Viral Ontology Network

leftover_blast

If BLAST fails this can identify the last completed match and provide the unfinished fasta file for completion.

lipase_reclassification

A proposed update for the classification and description of bacterial lipolytic enzymes

lsa_comparison

Files and scripts required to re-run the analysis described in the paper 'The BLAST and the spurious: Biases in genomic data propagate from heurstic local sequence alignment algorithms'.

mimic

A repository to generate minimal microbial consorita

mimic-1

Minimal Microbial Consortia creation tools

protologger

Protologgger is a tool for the description of novel taxa by providing taxonomic, functional and ecological insights

protologue-wiki

A repository of prokaryote descriptions, along with associated metadata, linked to GTDB.

qiime-deploy

Tool to easily install QIIME's dependencies on Linux systems

recon

REconstruction Of Novel culturable species

renamer

Gives each sequence in a FASTA file a unique name

rumen_mycoviruses

Analysis of the rumen mycoviral population

shannon_diversity_index

Calculates Shannon diversity index value for a dictionary of values

spherical

Spherical is an iterative approach to large metagenome assemblies, designed for clusters where insufficient RAM is available for a straightforward assembly.

split_fasta

Splits fasta file

sybilsbml

:exclamation: This is a read-only mirror of the CRAN R package repository. sybilSBML — SBML Integration in Package 'Sybil'