My bioinformatics daily scripts

This repository contains a sort of scripts for daily bioinformatics tasks.

N50 fasta statistics

The script N50_stats.py will give the stats of a draft genome:

Usage

N50_stats.py −f arrow/cgun_LG12.arrow.fa

Output

###### N50 stats #####

Assembly file name: pilon/cgun_LG12.pilon.fasta

Assembly size (bp): 22,504,182

Number of sequences: 8

Largest sequence: 9,135,553

N50 (bp): 6,574,633

L50: 2

Genomic circle plot with PyCairo

The script Circle_plot_pyCairo will create a genomic Circle plot using two tsv files:

• A expression fold change data with genomic location of each gene
• A Fst tsv file for each SNP with the genomic coordinates

Usage

./plot.py −e Gacu_FoldChange_GenomCoords.tsv −f batch_1.phistats_fw2−oc.tsv

where -e refers to the expression data and -f refers to the Fst data

Output