ggonnella

gfapy

Gfapy: a flexible and extensible software library for handling sequence graphs in Python

gfaviz

Graphical interactive tool for the visualization of sequence graphs in GFA format.

textformats

fastsubtrees

Python library and command line script , for fast extraction of subtrees of fairly large trees, consisting of millions of nodes, such as the NCBI taxonomy tree.

attrtables

System for storing, a dynamic set of entity attributes in a database

egcwebapp

A web application for visualizing and editing EGC data

multiplug

Flexible multi-language plugin system for Python

prenacs

Batch computing and results storage system with provenance-tracking

RiboPip

An alignment and analysis pipeline for Ribo-seq and RNA-seq data

scp-open

Open and edit a file on a remote server connected by ssh

snacli

Simplify writing dual use scripts for CLI and Snakemake

ec_finder

EcFinder: Python library and script to fuzzy search an enzyme EC number from an enzyme name

egc-spec

Specification for the Expected Genome Content format

egcgpt

Extract rules about the contents of prokaryotic genomes from scientific literature using GPT

egctools

Tools for handling the Expected Genome Content (EGC) Format

expectation_rules

A collection of expectations about the contents of prokaryotic genomes

fardes

Features Arrangement Description Miniformat

findconfig

Find a config file in XDG config paths, home directory or directories of the calling package

GFA-spec

Graphical Fragment Assembly (GFA) Format Specification

ggonnella

Config files for my GitHub profile.

giosc

R package with helper functions for ScRNA-seq analysis

git-batch-op

allows to run git repository operations on a group of repositories

lexpr

Lexpr: A simple logical expressions Lark-based parser

ntmirror

Local database mirroring NCBI taxonomy, kept up-to-date

pgcdo

Prokaryotic Genome Contents Definition Ontology

pgto

Prokaryotic Group Types Ontology

prost

`PROkaryote genome STatistics` (Prost): a system for the computation, storage and comparison of genomic data

quick-notes

Write synchronized single-lined notes from the command line

tabrec

Scripts for working with multiple record-type tabular files

urischemes

generating custom URI scheme handlers and install them