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Koeng101 / N_93-0.pileup
Created February 3, 2021 17:51
Example nanopore pileup
N 1 T 0 * *
N 2 T 0 * *
N 3 G 1 , /
N 4 T 2 ,, 7.
N 5 G 2 ,, <2
N 6 C 2 ,, 46
N 7 G 2 ,, A?
N 8 T 9 ,^5.^8.^].^>.^4.^],^],^], @:<E8<;1.
N 9 G 20 ,,.....,,,,,,,,,,,,, 7:8A=790.1550>518654
N 10 G 20 ,,.....,,,,,,,,,,,,, @84@>893:92>9>;/>;;:
@Koeng101
Koeng101 / distro.ipynb
Last active May 22, 2019 23:47
plan_jcvi_merge.ipynb
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@Koeng101
Koeng101 / jcvi_preexisting_merge.json
Last active May 23, 2019 17:37
[
{
"data": {
"wells": {
"post": [
{
"address": "A1",
"media": "lb",
"organism": "E.coli Top10",
"volume": 1200,
@Koeng101
Koeng101 / fix_vols.py
Last active June 11, 2019 07:26
A script to fix volumes in freegenes database
import json
import requests
r = requests.get('https://api.freegenes.org/wells/').json()
token = 'x'
headers = {'token': token}
for well in r:
if well['volume'] == None:
well_put = requests.put('https://api.freegenes.org/wells/{}'.format(well['uuid']), json={'volume': 50}, headers=headers)
print(well_put)
@Koeng101
Koeng101 / deepwell_to_plates.json
Created May 15, 2019 17:56
{"protocol-schema": "1.0.0", "metadata": {"protocolName": "Test 9 96", "author": "Keoni Gandall", "datetime": "2019-05-07 14:07:50.809415"}, "default-values": {"aspirate-flow-rate": {"p10_single": 5, "p10_multi": 5, "p50_single": 25, "p50_multi": 25, "p300_single": 150, "p300_multi": 150, "p1000_single": 500}, "dispense-flow-rate": {"p10_single": 10, "p10_multi": 10, "p50_single": 50, "p50_multi": 50, "p300_single": 300, "p300_multi": 300, "p1000_single": 1000}, "aspirate-mm-from-bottom": 1, "dispense-mm-from-bottom": 0.5, "touch-tip-mm-from-top": -1}, "robot": {"model": "OT-2 Standard"}, "pipettes": {"0bd11071-35e4-4ac2-a65a-fcd6d880539f": {"type": "pipette", "mount": "left", "name": "p50_multi", "model": "p50_multi_v1.3"}}, "labware": {"11_tip_box": {"slot": "11", "model": "opentrons-tiprack-300ul", "name": "11_tip_box"}, "trash_yo": {"slot": "12", "model": "fixed-trash", "name": "Trash yo"}, "cff3f61b-2ffc-48e9-a024-44abe6da9945": {"slot": "10", "model": "96-deep-well", "name": "deepwell_test"}, "a3da50ef-