Marco Galardini mgalardini

Computational biology, DIY music, small experiments

mgalardini / rsync_ecoli.sh

Last active August 29, 2015 13:57 — forked from nickloman/rsync_ecoli.sh

rsync -av rsync://ftp.ncbi.nlm.nih.gov/genomes/Bacteria --include "*/" --include "Bacteria/Escherichia*/*.fna" --exclude=* . --prune-empty-dirs

mgalardini / run_notebook

Last active August 29, 2015 14:07 — forked from davidshinn/ipnbdoctest.py

Allow longer run times

	#!/usr/bin/env python
	"""
	simple example script for running and testing notebook resulting in a new workbook.

	Usage: `run_notebook foo.ipynb foo_new.ipynb`

	Each cell is submitted to the kernel, and the outputs are compared with those stored in the notebook.
	Each cell is given half an hour to complete.
	"""

mgalardini / estimate-insert-sizes

Last active March 10, 2017 09:46 — forked from rchikhi/estimate-insert-sizes

Quickly estimates insert sizes of read datasets, given some sequence(s) they can be mapped to. Requires BWA. Short usage: <reference> <*.fastq>

+#!/usr/bin/env python
+doc = """
+Quickly estimates insert sizes of read datasets, given some sequence(s) they can be mapped to.
+Author: Rayan Chikhi
+short usage: <reference> <*.fastq>
+example:
+         estimate-insert-sizes contigs.fa readsA_1.fq readsA_2.fq readsB_1.fq readsB_2.fq