<![CDATA[BOL: SPAdes]]> https://bioinformaticsonline.com/bookmarks/view/27035/spades? https://bioinformaticsonline.com/bookmarks/view/27035/spades Tue, 19 Apr 2016 08:37:08 -0500 https://bioinformaticsonline.com/bookmarks/view/27035/spades <![CDATA[SPAdes]]> SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. This manual will help you to install and run SPAdes. SPAdes version 3.7.1 was released under GPLv2 on March 8, 2016 and can be downloaded from http://bioinf.spbau.ru/en/spades.

Manual at http://spades.bioinf.spbau.ru/release3.7.1/manual.html

Address of the bookmark: http://bioinf.spbau.ru/spades

]]> Abhimanyu Singh https://bioinformaticsonline.com/bookmarks/view/27035/spades#item-annotation-3146 Mon, 04 Dec 2017 07:39:59 -0600 https://bioinformaticsonline.com/bookmarks/view/27035/spades#item-annotation-3146 <![CDATA[Comment by Jit]]> Common usage 

SPAdes: de Bruijn graph based assembler

The last assembler we will run is SPAdes. SPAdes is different from the other assemblers in that it generates a final assembly from multiple kmers. A list of kmers is automatically selected by SPAdes using the maximum read length of the input data, and each individual kmer contributes to the final assembly. To run SPAdes we will use the spades.py command with the --careful option to minimize the number of mismatches in the contigs, -o for the output folder, -1 for the path to the forward reads, -2 for the path to the reverse reads, and -s for the path to the singles reads. If desired, a list of kmers can be specified with the -k flag which will override automatic kmer selection.

spades.py --careful -o SPAdes_out -1 /common/Assembly_Tutorial/Quality_Control/Sample_1.fastq -2 /common/Assembly_Tutorial/Quality_Control/Sample_2.fastq -s /common/Assembly_Tutorial/Quality_Control/Sample_s.fastq

 

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