Haruo Suzuki (haruo[at]g-language[dot]org)
Last Update: 2016-04-26
微生物ゲノム配列解析
Pan-genome解析の演習
Rスクリプトscripts/test_gene_content.R
は、gene content(遺伝子の有無)データ行列を作成し、Pan-genome解析(共有遺伝子、ベン図、クラスター分析)を行なう。Rスクリプトの実行例は以下の通り:
Rscript --vanilla scripts/test_gene_content.R
微生物ゲノム解析の概要
- 参考文献
- Tools for bacterial comparative genomics | Holt Lab
- Inside the Pan-genome - Methods and Software Overview. Curr Genomics. 2015 Aug
- A brief review of software tools for pangenomics. Genomics Proteomics Bioinformatics. 2015 Feb
- ITEP: an integrated toolkit for exploration of microbial pan-genomes. BMC Genomics. 2014 Jan
- Computing for Comparative Microbial Genomics, Springer, 2009, 270p.
-
Tools for bacterial comparative genomics | Holt Lab http://holtlab.net/2015/02/25/tools-for-bacterial-comparative-genomics/
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Bacterial genomics tutorial | Holt Lab https://holtlab.net/2014/12/27/bacterial-genomics-tutorial-2/
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Bacterial genomics tutorial | BacPathGenomics https://bacpathgenomics.wordpress.com/2013/04/13/bacterial-genomics-tutorial/
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Beginner's guide to comparative bacterial genome analysis using next-generation sequence data. Microb Inform Exp. 2013. http://www.ncbi.nlm.nih.gov/pubmed/23575213
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Ten years of pan-genome analyses. Curr Opin Microbiol. 2015 Feb http://www.ncbi.nlm.nih.gov/pubmed/25483351
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rarefaction curve
-
plot - accumulation curve in R - Stack Overflow http://stackoverflow.com/questions/21615628/accumulation-curve-in-r
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Vegan: ecological diversity https://cran.r-project.org/web/packages/vegan/vignettes/diversity-vegan.pdf
-
Gene accumulation curves in R | smoke&umami http://smokeandumami.com/2010/01/21/gene-accumulation-curves-in-r/
-
自前でrarefactionカーブ in R http://tullbergia.at.webry.info/201009/article_3.html
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自前でrarefactionカーブ in R vol.2: マルチコア対応 http://tullbergia.at.webry.info/201111/article_1.html
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データ解析|種多様性の測定|希薄化曲線(rarefaction curves)|上の計算を R で行うためのコード http://www.lab2.toho-u.ac.jp/sci/bio/theoeco/wiki/index.php?plugin=attach&pcmd=open&file=jissyusyo_DA.pdf&refer=2013%CC%EE%B3%B0%C0%B8%C2%D6%B3%D8%BC%C2%BD%ACI
- de Bruijn Graph
- de Bruijn Graph を使った de novo アセンブリの発想がすごい件 - ほくそ笑む
- CLCバイオジャパン - De Novo アセンブリ
- "de Bruijn"はどう発音する? - Wolfeyes Bioinformatics beta
- de Bruijn graphを使ったアセンブラーのヘテロなサイトの取り扱いについて - #LSQA 質問日 Aug 31 '12
The shell script scripts/run.sh
automatically carries out the entire steps: creating subdirectories, downloading data files, and running the R scripts.
Let's run the driver script in the project's main directory mgsa/
with:
bash scripts/run.sh > log.txt 2>&1 &
Created the project directory using mkdir -p ./{data,scripts,analysis}
mv Rplots.pdf table.csv analysis/
マイコプラズマ菌(Mycoplasma genitalium)のコンプリートゲノム配列の取得方法
プロジェクト・ディレクトリを作成し移動:
mkdir -p ~/projects/mgsa/data
cd ~/projects/mgsa/data
"Mycoplasma genitalium"のゲノム配列データのFTPディレクトリパス(URL)を記載したファイルをwget
でダウンロードする:
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/Mycoplasma_genitalium/assembly_summary.txt
または
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/Mycoplasma_genitalium/assembly_summary.txt
ゲノム配列解読の状況 Status (assembly_level
) を確認:
head -n 1 assembly_summary.txt | cut -f12
grep -v '^#' assembly_summary.txt | cut -f12 | sort | uniq -c
出力例:
assembly_level
5 Complete Genome
1 Contig
"Complete Genome"のデータ最新版(version_status = latest
)のURLを抽出する:
ftpdirpaths=($(awk -F "\t" '$12=="Complete Genome" && $11=="latest"{print $20}' assembly_summary.txt))
または
ftpdirpaths=($(grep "latest.*Complete Genome" assembly_summary.txt | cut -f20))
抽出されたURLの数を確認する:
echo ${#ftpdirpaths[@]}
echo ${ftpdirpaths[@]}
データの圧縮ファイル(.fna.gz,.faa.gz)をwget
でダウンロードする:
for URL in ${ftpdirpaths[@]}
do
wget -nv $URL/{*.fna.gz,*.faa.gz}
done
gunzip
コマンドで解凍:
gunzip *.gz
参考: https://github.com/haruosuz/mgen ケーススタディ https://dl.dropboxusercontent.com/u/33495171/introBI/CaseStudy.md.html NCBI assembly summary
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Genomes Download FAQ
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12. How can I download RefSeq data for all complete bacterial genomes?
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9. How can I find the sequence and annotation of my genome of interest? Using the assembly summary files for bacteria or a species under genbank or refseq
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ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/assembly_summary.txt
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ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt
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ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/Mycoplasma_genitalium/assembly_summary.txt
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ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/Mycoplasma_genitalium/assembly_summary.txt
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Genomic nucleotide composition
cd data/
ls -lh
# Working with Gzipped Compressed Files using gzcat, zgrep, and zless
gzcat *.fna.gz | head -n 2
zgrep -c '^>' *.gz
zless *.faa.gz