Shulou(Shulou.com)06/01 Report--

In this issue, the editor will bring you about how to understand the genome assembly software spades. The article is rich in content and analyzes and narrates it from a professional point of view. I hope you can get something after reading this article.

Spades, a de novo genome assembly software, is suitable for the assembly of small genomes such as bacteria / fungi, but is not recommended for the assembly of animal and plant genomes. The software is mainly used for illumina,IonTorrent reads assembly, and can also be used for PacBio, Oxford nanopore, Sanger reads assembly.

The official website is as follows

Http://cab.spbu.ru/software/spades/

Spades is a set of software, similar to the office office software series, which contains the following five executable files

MetaSPAdes

PlasmidSPAdes

RnaSPAdes

TruSPAdes

DisSPAdes

MetaSPAdes is used to assemble metagenomic data, plasmidSPAdes is used to assemble chloroplast / mitochondrial genomes, rnaSPAdes is used to assemble RNA-seq data, truSPAdes is used to assemble treseq barcode sequences, and disSPAdes is used to assemble diploid genomes with high heterozygosity.

The installation process of the software is as follows

Wget http://cab.spbu.ru/files/release3.12.0/SPAdes-3.12.0-Linux.tar.gztar xzvf SPAdes-3.12.0-Linux.tar.gzcd SPAdes-3.12.0-Linux

Download the binary package directly from the official website and decompress it. In the bin directory, there are many executable files

. / ├── dipspades.py ├── metaspades.py-> spades.py ├── plasmidspades.py-> spades.py ├── rnaspades.py-> spades.py ├── spades-bwa ├── spades-core ├── spades-corrector-core ├── spades-dipspades-core ├── spades-gbuilder ├── spades-gmapper ├── spades-hammer ├── spades_init.py ├── spades_init.pyc ├── spades-ionhammer ├── spades-kmercount ├── spades. Py ├── spades-truseq-scfcorrection └── truspades.py

Spades.py is the main submission script, and the software supports a variety of sequencing types.

Single-ended data

Use the-- S1 parameter to specify the sequence files that are sequenced separately. If there are multiple libraries, use a numeric suffix to distinguish them, such as-- s _ 1 ~ m ~ 2.

Double-ended data

Use-- pe1-1 and-- pe1-2 to specify R1-and R2-terminal sequence files for double-ended sequencing, respectively. Multiple libraries are distinguished by numeric suffixes, such as-- pe2-1,-- pe2-2.

The basic usage is as follows:

Spades.py-k 21 pe1 33 spades_output 5 5 spades.py 77 99127-careful-- pe1-1 R1.fastq-- pe-2 R2.fastq-o spades_output

The output result directory generates many files, where scaffolds.fasta corresponds to the result of scaffold and contig.fasta corresponds to the result of contig assembly.

The above is how to understand the genome assembly software spades shared by the editor. If you happen to have similar doubts, you might as well refer to the above analysis. If you want to know more about it, you are welcome to follow the industry information channel.

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