SPAdes

The current version of SPAdes works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. You can also provide additional contigs that will be used as long reads.

Install

wget https://cab.spbu.ru/files/hicSPAdes/hicSPAdes-binner-0.1.tar.gz
tar -xzf hicSPAdes-binner-0.1.tar.gz
cd hicSPAdes-binner-0.1
mkdir build 
cd build 
cmake ../src -Wno-dev
make hicspades-binner

wget https://cab.spbu.ru/files/release3.15.4/SPAdes-3.15.4-Linux.tar.gz
tar -xzf SPAdes-3.15.4-Linux.tar.gz

export PATH=/mnt/d/WSL_dir/workdir/hicSPAdes-binner-0.1/build/bin:/mnt/d/WSL_dir/workdir/hicSPAdes-binner-0.1/build/SPAdes-3.15.4-Linux/bin:$PATH

SPAdes

Usage

spades.py -o out_dir  -1 E.R1.fq.gz  -2 E.R2.fq.gz    
spades.py -o out_dir  -1 E.R1.fq.gz  -2 E.R2.fq.gz   --pacbio   E.pacbio.fq.gz
spades.py -o out_dir  -1 E.R1.fq.gz  -2 E.R2.fq.gz   --nanopore E.nano.fq.gz

# --careful --disable-gzip-output --threads 24 --memory 150(是GB)   

得到默认命名的scaffolds.fasta，可以重新命名; 其中输出的Header示例：

>NODE_1_length_535588_cov_260.739

## 可以基于此筛选：放弃coverage<30的序列，length<500的序列

也可以加入其它软件生成的contigs（作为seed?）：

--trusted-contigs      high_quality_ctgs.fa
--untrusted-contigs    low_quality_ctgs.fa

Other Modes

  --isolate                   this flag is highly recommended for high-coverage isolate and multi-cell data
  --sc                        this flag is required for MDA (single-cell) data
  --meta                      this flag is required for metagenomic data
  --bio                       this flag is required for biosyntheticSPAdes mode
  --corona                    this flag is required for coronaSPAdes mode
  --rna                       this flag is required for RNA-Seq data
  --plasmid                   runs plasmidSPAdes pipeline for plasmid detection
  --metaviral                 runs metaviralSPAdes pipeline for virus detection
  --metaplasmid               runs metaplasmidSPAdes pipeline for plasmid detection in metagenomic datasets (equivalent for --meta --plasmid)
  --rnaviral                  this flag enables virus assembly module from RNA-Seq data
  --iontorrent                this flag is required for IonTorrent data

coronaspades.py
metaplasmidspades.py
metaspades.py
metaviralspades.py
plasmidspades.py
rnaspades.py
rnaviralspades.py
truspades.py

示例：

spades.py -o out_dir  -1 E.R1.fq.gz  -2 E.R2.fq.gz  --meta  
## Same As ##
metaspades.py  -o out_dir  -1 E.R1.fq.gz  -2 E.R2.fq.gz

hicSPAdes (Meta)

Hi-C Metagenomics, pre-release.

批量调用

• Batch.py批量生成脚本与yaml
• Collect.py将每个样本的fasta分开至每一个bin

## 需要修改Gen_Scripts开头的PATH！！！

python3 Batch.py clean.fq.lst

其中clean.fq.lst示例：

Example1    ABSOLUTE_PATH//E1_R1.fq.gz ABSOLUTE_PATH//E1_R1.fq.gz
Example2    ABSOLUTE_PATH//E2_R1.fq.gz ABSOLUTE_PATH//E2_R1.fq.gz

<output_dir(also as perfix)>   <clean_R1.fq.gz>    <clean_R2.fq.gz>
- tab分隔, 无header
- output_dir末尾不能带'/'等影响linux命名的字符，它可以是相对or绝对路径；建议使用分析名当文件夹
- 生成：output_dir.pipe.sh  output_dir/cleandata.yaml 

示例bash

Example1.pipe.sh

cd Example1
export PATH=/mnt/d/WSL_dir/workdir/hicSPAdes-binner-0.1/build/bin/:$PATH
export PATH=/mnt/d/WSL_dir/workdir/hicSPAdes-binner-0.1/build/SPAdes-3.15.4-Linux/bin/:$PATH
metaspades.py -1 ABSOLUTE_PATH/E1_R1.fq.gz -2 ABSOLUTE_PATH/E1_R1.fq.gz -o .
hicspades-binner assembly_graph_with_scaffolds.gfa cleandata.yaml Bins
cd Bins ; python3 /mnt/d/WSL_dir/workdir/Collect.py; cd ..

示例yaml

Example1/cleandata.yaml

        [
                {
                        orientation: "fr",
                        type: "hic",
                        right reads: ["ABSOLUTE_PATH/E1_R1.fq.gz"],
                        left reads: ["ABSOLUTE_PATH/E1_R1.fq.gz"],
                }
        ]

‘hicSPAdes-binner currently supports a single Hi-C library described in a YAML file’, 安全起见一个样本一个YAML吧

Error

No input file to read network 

• 因为并行运行使用同一个./tmp目录，导致结果相互覆盖
• 数据不足，没有通过HiC数据连接的contigs

参考

SPAdes: https://github.com/ablab/spades
hicSPAdes: https://cab.spbu.ru/software/hicspades/
SPAdes manual: https://cab.spbu.ru/files/release3.13.0/manual.html SPAdes: https://zhuanlan.zhihu.com/p/77274286