felipelira Goto Github PK

cvtree

A whole-genome and alignment-free prokaryotic phylogeny tool

extract_plasmids

Detect and extract plasmids in fragmented (draft) genomes.

fastq-fastq_stats

fastq-stats_fastq

files_to_test

Files used to test scripts

fripan

Interactive, web tool for exploring pan-genome of bacterial strains

genome_updater

Automatic download and update genome and sequences files from NCBI

get_core_proteomes

Get_core_proteomes.py calculates the similarity distances based on k-mers using the core proteomes of species/strains.

get_photo

Download photos from Flickr using keywords.

get_phylomarkers

A pipeline to select optimal markers for microbial phylogenomics, population genetics and genomic taxonomy

get_plasmids

Detect and extract plasmids in fragmented (draft) genomes.

isfinder_database

download isfinder database

multifasta2dict

Concatenate multifasta files and create a tabular file containing information about their origins.

post-processing-antismash

Post-process of results in the output folder created by Antismash

post_processing_get_homologues

Scripts to process results generated by get_homologues

predipath

PrediPath

python

Sort of scripts created for specific proposes during the elaboration and development of complete pipelines for microbiomes, genomics, and metagenomics sequencing data.

r

R scripts created to specific proposes to make easy my/your life.

roary

Rapid large-scale prokaryote pan genome analysis

select-seed-seqs

snippy

:scissors: :zap: Rapid haploid variant calling and core genome alignment

squeezemeta

A complete pipeline for metagenomic analysis

update_genome_collection

Script to download and update a collection of genomes based on a dynamic list of taxa.