bede

Comparing coverage & abundance estimates using Grate, and on-target length distributions

Objectives:

• 'Fish' for reference genomes in demultiplexed FASTQs for one or more experimental conditions (i.e. Prom runs).
• Plot estimated coverage and abundance by target genome, and condition/barcode.
• Calculate the length distributions of Zepto reads between conditions/barcodes.

1. Fetch data

e.g. a run from CLIMB object storage

aws s3 sync s3://quick-research-bede-storage/runs-cat/DS_NEBtagged_sequenase_Zepto_18_11_2025 DS_NEBtagged_sequenase_Zepto_18_11_2025

bede

$ RUSTFLAGS="-C target-cpu=native" cargo +nightly run -r -- --threads 32
   Compiling dna-rank v0.1.0 (/data32/dna-rank)
    Finished `release` profile [optimized + debuginfo] target(s) in 3.17s
     Running `target/release/bench --threads 32`
n = 100000
Ranker                                                         bits |     1t               |     6t               |
                                                                    | latncy   loop stream | latncy   loop stream |
Ranker<Plain128, TrivialSB, WideSimdCount2, false>            4.00b |   15.3    3.9    4.2 |    0.6    0.2    0.2 |
Ranker<Plain256, TrivialSB, SimdCountSlice, false>            3.01b |   21.4   10.3   11.0 |    0.8    0.6    0.6 |
Ranker<Plain512, TrivialSB, SimdCountSlice, false>            2.51b |   24.1   15.6   16.5 |    1.0    0.8    0.8 |

bede

bede

22,23c22,23
< \documentclass[unnumsec,webpdf,contemporary,large]{oup-authoring-template}%
< %\documentclass[unnumsec,webpdf,contemporary,large,namedate]{oup-authoring-template}% uncomment this line for author year citations and comment the above
---
> % \documentclass[unnumsec,webpdf,contemporary,large]{oup-authoring-template}%
> \documentclass[unnumsec,webpdf,contemporary,large,namedate]{oup-authoring-template}% uncomment this line for author year citations and comment the above
957,958c957,958
< %\bibliographystyle{abbrvnat}
< %\bibliography{reference}
---

bede

"""
Purpose: Concatenate demultiplexed FASTQs by barcode for one or more ONT runs
Usage: python concat_by_barcode.py run1/fastq_pass run2/fastq_pass -o output/
Author: Bede Constantinides
"""
import subprocess
import sys
import argparse
from collections import defaultdict
from pathlib import Path

bede

from io import StringIO

import pandas as pd
import pandera as pa
import pandera.extensions as extensions
from pandera.typing import Index, Series

csv_string = """
sample_name,country,region
cDNA-VOC-1-v4-1,USA,Bretagne

bede

def split_summary_by_barcode(summary_path, out_dir, run_name):
    '''Given a sequencing summary file path, write per barcode summaries to an output directory'''
    
    dtypes = {
        'filename_fastq': 'object',
        'filename_fast5': 'object',
        'read_id': 'object',
        'run_id': 'category',
        'channel': 'int64',
        'mux': 'int64',

bede

import pandas as pd
from bokeh.models.widgets import Select
from bokeh.layouts import widgetbox
from bokeh.models import ColumnDataSource, DataTable, TableColumn, CustomJS
from bokeh.io import show, output_file, output_notebook, reset_output
from bokeh.layouts import row, column, layout


raw_data = {'ORG': ['APPLE', 'ORANGE', 'MELON'],
        'APPROVED': [5, 10, 15],

bede

import pandas as pd
from scipy.spatial.distance import squareform
from scipy.cluster.hierarchy import fcluster, linkage

def cluster_df(df, method='single', threshold=100):
    '''
    Accepts a square distance matrix as an indexed DataFrame and returns a dict of index keyed flat clusters 
    Performs single linkage clustering by default, see scipy.cluster.hierarchy.linkage docs for others
    '''
   

bede

FROM ubuntu:16.04

RUN apt-get update && \
	apt-get --yes install \
	kmc smalt python3-pip zlib1g-dev libncurses5-dev libncursesw5-dev mummer samtools 

RUN pip3 install iva

ENTRYPOINT ["iva"]