加载中…使用SPAdes软件对基因组进行拼接
(2015-08-04 09:56:21)
标签：
it |
分类： 生物信息学 |
1:网址：http://bioinf.spbau.ru/spades#benchmark
Contigs
of the same genome, quality of which is average or unknown. Contigs
of poor quality can be used but may introduce errors in the
assembly. This option is also not intended for contigs of the
related species.
spades.py
--untrusted-contigs assembly_out_velvet/contigs.fa -k
21,23,25,27,29,31,33,47,51,55,77,81,83,85,87,97 --cov-cutoff auto
--careful -1 correct .1_1.fastq.paired.fq -2
correct.1_2.fastq.paired.fq -o spades_erro
2:可以拼接来自多个平台的测序数据，如果只有一个库，可以利用来自不同的软件的组装结果（参见软件参数：--untrusted-contigs或），除了不兼容Illumina与IonTorrent文库的混合文库拼接外，其他的平台数据不同文库都可以实现混合拼接。
--trusted-contigs 4:参数：（http://spades.bioinf.spbau.ru/release3.5.0/manual.html#sec3.4）
-1 forward reads
-2 reverse reads
Tries to reduce the number of mismatches and short
indels. Also runs MismatchCorrector – a post processing tool, which
uses tool
(comes with SPAdes) .
This option is recommended.
--pacbio
File
with PacBio CLR reads.
--trusted-contigs
Reliable
contigs of the same genome, which are likely to have no
misassemblies and small rate of other errors (e.g. mismatches and
indels). This option is not intended for contigs of the related
species.
--untrusted-contigs
实际例子：
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