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doc/pacbio_consensus.md  view on Meta::CPAN

sge_option_pda =
sge_option_pla =
sge_option_fc =
sge_option_cns =

pa_concurrent_jobs = 4
ovlp_concurrent_jobs = 4

pa_HPCdaligner_option =  -v -B4 -t16 -e.70 -l1000 -s1000
ovlp_HPCdaligner_option = -v -B4 -t32 -h60 -e.96 -l500 -s1000

pa_DBsplit_option = -x500 -s50
ovlp_DBsplit_option = -x500 -s50

falcon_sense_option = --output_multi --min_idt 0.70 --min_cov 4 --max_n_read 200 --n_core 2

overlap_filtering_setting = --max_diff 100 --max_cov 100 --min_cov 20 --bestn 10 --n_core 2

EOF

#real    274m19.701s
#user    2202m51.987s
#sys     1737m17.436s
time fc_run fc_run.cfg

#N50     791352
#S       12094794
#C       39
faops n50 -S -C 2-asm-falcon/p_ctg.fa
```

## Atha Col-0

https://www.ncbi.nlm.nih.gov/sra?LinkName=biosample_sra&from_uid=4539665

## 复活草

## Atha Ler-0

* 三代原始数据

```bash
cd ~/data/pacbio/rawdata/
perl ~/Scripts/download/list.pl -u https://downloads.pacbcloud.com/public/SequelData/ArabidopsisDemoData/
perl ~/Scripts/download/download.pl -a -i public_SequelData_ArabidopsisDemoData.yml

aria2c -x 9 -s 3 -c -i /home/wangq/data/pacbio/rawdata/public_SequelData_ArabidopsisDemoData.yml.txt
```

`.subreads.bam` to fasta

```bash
mkdir -p $HOME/data/pacbio/rawdata/ler0_test/fasta
cd $HOME/data/pacbio/rawdata/ler0_test/fasta

samtools fasta \
    ~/data/pacbio/rawdata/public/SequelData/ArabidopsisDemoData/SequenceData/1_A01_customer/m54113_160913_184949.subreads.bam \
    > m54113_160913_184949.fasta

samtools fasta \
    ~/data/pacbio/rawdata/public/SequelData/ArabidopsisDemoData/SequenceData/3_C01_customer/m54113_160914_092411.subreads.bam \
    > m54113_160914_092411.fasta

#N50     70763
#S       10753458447
#C       1135065
faops n50 -C -S *.fasta
```

## 其它模式生物

用这篇文章里提供的样例, doi:10.1038/sdata.2014.45.

# 其它相关的程序

https://github.com/PacificBiosciences/DevNet/wiki/Compatible-Software

## PacBio 自产

* HGAP: Hierarchical Genome Assembly Process，层次基因组组装, 以相对较长的读长数据为种子 (Seeding Reads),
  以相对较短的读长数据用于内部纠错. 这个时候得到的读长数据足够长也足够准确, 完全可以用于 de novo 组装,
  而无需二代数据帮忙. Falcon 可以认为是 HGAP 的后续版本.
* PBJelly: 用于 gap closing,
  [这里有简介](https://github.com/alvaralmstedt/Tutorials/wiki/Gap-closing-with-PBJelly).

## 混合组装

* [DBG2LOC](http://www.nature.com/articles/srep31900) - 加上纯二代程序 Platanus (SOAP/ABySS)
* ECtools: 用二代的 contigs 代替 reads 来校正三代, 是很多 python 脚本的集合, 现在基本停止发展
* [quickmerge](https://github.com/mahulchak/quickmerge) - 合并纯三代组装与二三代混合组装

# 中文资料

[生物通上有个专题](http://www.ebiotrade.com/custom/ebiotrade/zt/130503/index.htm), 有点老,
但基本的内容还是不错的.

生物通上近期还有两篇文章也挺好

* [韩国人基因组](http://www.ebiotrade.com/newsf/2016-10/2016108164502500.htm)
* [Atha Ler-0](http://www.ebiotrade.com/newsf/2016-9/201693094511949.htm)