ABySS (2019.3) - 短序列拼接

1. 简介

ABySS 是用于从头拼接双端测序短序列或较大基因组的软件，官网有测试数据可以使用。

2. 下载安装

ubantu下载安装。

sudo apt-get install abyss

3. 参数详解

• abyss 将 short reads 组装成 contigs

• abyss-pe 将 short reads 组装成 contigs 和 scaffolds

• --chastity 去除污染的reads默认选项

• --no-chastity 不去除污染的reads

• --trim-masked 从序列某端去除低质量的碱基，默认选项

• --no-trim-masked 不从序列末端去除低质量碱基

• -q | --trim-quality=N 从序列尾端去除碱基质量低于此值的碱基

• --standard-quality 碱基质量格式为 phred33 ，默认选项

• --illumina-quality 碱基质量格式为 phred64

• -o | --out=FILE 输出的 contigs 文件的文件名

• -k | --kmer=N k-mer 长度，必要参数

• -t | --trim-length=N maximum length of dangling edges to trim

• -c | --coverage=FLOAT 去除 k-mer 覆盖读低于此值的 contigs

• -b | --bubbles=N pop bubbles shorter than N bp [3*k]

• -b0 | --no-bubbles do not pop bubbles

• name 指定生成文件的前缀，运行结束后，会生成很多文件，主要关注test-contigs.fa，test-scaffolds.fa

4. 示例

使用 abyss-pe 将 1 个 paired-end 文库的short reads 组装成 scaffolds

wget http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/1.3.4/test-data.tar.gz
tar xzvf test-data.tar.gz
abyss-pe \
k=25 --out=test name=test \
 in='test-data/reads1.fastq test-data/reads2.fastq'

Assembling multiple libraries

abyss-pe \
k=25 --out=test name=ecoli \
lib='pea peb' \
 pea='pea_1.fa pea_2.fa' \
 peb='peb_1.fa peb_2.fa' \
 se='se1.fa se2.fa'

使用多个 k 值进行基因组组装，再寻找最佳 k 值：

export k
for k in {20..40}; do
 mkdir k$k
 abyss-pe -C k$k name=ecoli in=../reads.fa
 done
abyss-fac k*/ecoli-contigs.fa

通过for 循环，实现多 梯度kmer组装：

for k in `seq 50 8 90`; do
 mkdir k$k
 abyss-pe -C k$k name=test k=$k in=reads.fa
done

其他

Scaffolding

Scaffolding with linked reads

Rescaffolding with long sequences

Assembling using a Bloom filter de Bruijn graph

Assembling using a paired de Bruijn graph

Assembling a strand-specific RNA-Seq library

Parallel processing

Running ABySS on a cluster

Using the DIDA alignment framework

Tips

abyss-pe是一种Makefile驱动程序脚本，因此任何的make选项均可与abyss-pe一起连用：

• ABYSS: de Bruijn graph assembler

• ABYSS-P: parallel (MPI) de Bruijn graph assembler

• AdjList: find overlapping sequences

• DistanceEst: estimate the distance between sequences

• MergeContigs: merge sequences

• MergePaths: merge overlapping paths

• Overlap: find overlapping sequences using paired-end reads

• PathConsensus: find a consensus sequence of ambiguous paths

• PathOverlap: find overlapping paths

• PopBubbles: remove bubbles from the sequence overlap graph

• SimpleGraph: find paths through the overlap graph

• abyss-fac: calculate assembly contiguity statistics

• abyss-filtergraph: remove shim contigs from the overlap graph

• abyss-fixmate: fill the paired-end fields of SAM alignments

• abyss-map: map reads to a reference sequence

• abyss-scaffold: scaffold contigs using distance estimates

• abyss-todot: convert graph formats and merge graphs

需要加载到PATH环境变量中，如配置ABYSS：

export abyss_home=~/soft/abyss-...
​export PATH=$abyss_home/ABYSS:$PATH

source ~/.bashrc