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# Tuning parameters for the dataset of *E. coli*

[TOC level=1-3]: # " "
- [Tuning parameters for the dataset of *E. coli*](#tuning-parameters-for-the-dataset-of-e-coli)
- [More tools on downloading and preprocessing data](#more-tools-on-downloading-and-preprocessing-data)
    - [Extra external executables](#extra-external-executables)
    - [Two of the leading assemblers](#two-of-the-leading-assemblers)
    - [PacBio specific tools](#pacbio-specific-tools)
- [*Escherichia coli* str. K-12 substr. MG1655](#escherichia-coli-str-k-12-substr-mg1655)
    - [Download](#download)
    - [Preprocess Illumina reads](#preprocess-illumina-reads)
    - [Preprocess PacBio reads](#preprocess-pacbio-reads)
    - [Reads stats](#reads-stats)
    - [Spades](#spades)
    - [Platanus](#platanus)
    - [Quorum](#quorum)
    - [Down sampling](#down-sampling)
    - [Generate k-unitigs (sampled)](#generate-k-unitigs-sampled)
    - [Create anchors (sampled)](#create-anchors-sampled)
    - [Merge anchors with Qxx, Lxx and QxxLxx](#merge-anchors-with-qxx-lxx-and-qxxlxx)
    - [Merge anchors](#merge-anchors)
    - [Scaffolding with PE](#scaffolding-with-pe)
    - [Different K values](#different-k-values)
    - [3GS](#3gs)
    - [Local corrections](#local-corrections)
    - [Expand anchors](#expand-anchors)
    - [Final stats](#final-stats)


# More tools on downloading and preprocessing data

## Extra external executables

```bash
brew install aria2 curl                     # downloading tools

brew install homebrew/science/sratoolkit    # NCBI SRAToolkit

brew reinstall --build-from-source --without-webp gd # broken, can't find libwebp.so.6
brew reinstall --build-from-source gnuplot@4
brew install homebrew/science/mummer        # mummer need gnuplot4

brew install openblas                       # numpy

brew install python
pip install --upgrade pip setuptools
pip install matplotlib
brew install homebrew/science/quast         # assembly quality assessment
quast --test                                # may recompile the bundled nucmer

# canu requires gnuplot 5 while mummer requires gnuplot 4
brew install --build-from-source canu

brew unlink gnuplot@4
brew install gnuplot
brew unlink gnuplot

brew link gnuplot@4 --force

brew install r --without-tcltk --without-x11
brew install kmergenie --with-maxkmer=200
```

## Two of the leading assemblers

```bash
brew install homebrew/science/spades
brew install wang-q/tap/platanus

```

## PacBio specific tools

PacBio is switching its data format from `hdf5` to `bam`, but at now
(early 2017) the majority of public available PacBio data are still in
formats of `.bax.h5` or `hdf5.tgz`. For dealing with these files, PacBio
releases some tools which can be installed by another specific tool,
named `pitchfork`.

Their tools *can* be compiled under macOS with Homebrew.

* Install some third party tools

```bash
brew install md5sha1sum
brew install zlib boost openblas