mgalardini

#!/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

mgalardini

#!/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

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