mxmader

import requests
import json

####
# inputs
####
username = ''

# from https://github.com/user/settings/tokens
token = ''

darencard

Useful Genomics Oneliners

The following commands sometimes require non-standard software like bioawk and seqtk.

rename scaffold headers with sequential numbers and lengths ("scaffold-N ")

bioawk -c fastx '{ print ">scaffold-" ++i" "length($seq)"\n"$seq }' < genome.fasta > new_genome.fasta

make association table of old and renamed scaffold names after above renaming command

lmakarov

'use strict';
exports.handler = (event, context, callback) => {

    // Get request and request headers
    const request = event.Records[0].cf.request;
    const headers = request.headers;

    // Configure authentication
    const authUser = 'user';
    const authPass = 'pass';

retorquere

#!/usr/bin/env python3

import zipfile
import sys
import re
import xml.etree.ElementTree as ET

namespaces = {
  'a': 'http://schemas.openxmlformats.org/drawingml/2006/main',
  'r': 'http://schemas.openxmlformats.org/officeDocument/2006/relationships',

rchikhi

Wheeler graphs

Gagie, Manzini, Siren
Theoretical Computer Science, 2017
https://www.sciencedirect.com/science/article/pii/S0304397517305285

Notes of a whiteboard presentation to the Bonsai team in Lille.
These notes largely follow the paper.
Rayan Chikhi, 2019