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kPALの使い方

More than 5 years have passed since last update.

最近Genome Biologyで出た、k-merベースで実験のQCを行うツール、
kPAL(Python)のチュートリアル(http://kpal.readthedocs.org/en/latest/tutorial.html
)にざっと目を通した。

kPALのインストール

pip install kPAL

または

git clone https://github.com/LUMC/kPAL.git
cd kPAL
pip install -e .

kPALの使い方

ヘルプの表示

kpal -h

テストデータをダウンロード

wget http://kpal.readthedocs.org/en/latest/_downloads/tutorial.zip
unzip tutorial.zip
cd tutorial
# a_1.fa, a_2.fa, b_1.fa, b_2.fa, c_1.fa, c_2.fa, d_1.fa, d_2.faの8つのfastaファイル(4ペア)がある事を確認
ls

8-merで解析、1側のfastaファイルの結果を、reads1.k8に保存

kpal count -k 8 *_1.fa reads_1.k8

reads_1.k8はバイナリファイルで、kpal infoで中身が確認できる

kpal info reads_1.k8

_2側も同様に

kpal count -k 8 *_2.fa reads_2.k8

_1側と_2側の結果をマージして、merged.k8に保存

kpal merge reads_1.k8 reads_2.k8 merged.k8

マージ結果は、以下のように確認できる(マージされると_で名前が連結されるらしい)

kpal info merged.k8 -p c_1_c_2

k-merベースでのサンプル間の距離

kpal distance reads_1.k8 reads_2.k8 -l c_1 -r c_2

総当たりでの距離

kpal matrix merged.k8 -
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