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adna2019

Exercises and slides for F stats and admixture graphs

alienaliencontamination

The script obtain the frequency of nucleotides

analysis_vampirebats

calculate_depthbreath

The function calculate the depth and breath of coverage, based in depth samtools output.

count_nucleotides

This script count the number of nucleotides that you have in your fasta file

densityplots

depthplots

This script compare depth between samples

diffrences_snps

The script compare the number of difference SNPs between sample

heatmap_breath

This script draw a heat map depens the breath of coverage pf your samples

match_id-genomesequence

Recover "correct" genome sequence of the db

mergeids.py

This script read a fasta file where you have more than one sequence with the same ID and you need to merge this sequences by ID

mixtures

This script identify if we have a mixture of pathogens in the sample data

mobiseq.sh

Pipeline to analyze data from the MobiSeq method. https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12984

mobiseq_humans.sh

Pipeline to analyze MobiSeq data generated from modern and ancient human samples

planetas

Clase de Github Escuela de Verano de Bioinformatica Qro 2016

planets

Clase Github Verano Bioinformatica 2016

reversetraslation

Reverse traslation Protein to DNA based on your codon table

riceblast_effectoranalysis

Part of the code used for the paper Latorre et al.

thesis

transposon_calling

vcf_to_snpstable

This script read and convert a multiple vcf file to an effectors table