The denovo assembly output of metagenomics data may have hundreds of Contigs！ Is it means that different contigs represent different species ?
*Getting this error: /Users/lindakohn/Desktop/tools/SPAdes-3.7.1-Darwin/bin/spades.py -k 21,33,55,77 --careful --only-assembler --pe<#>-12 <euro_plasmid_r1_paired.fastq euro_plasmid_r2_paired.fastq=""> --pe<#>-s1 <euro_plasmid_r1_unpaired.fastq> --pe<#>-s2 <euro_plasmid_r2_unpaired.fastq> -o Euro_plasmid_spades_output
-bash: syntax error near unexpected token `newline' what is wrong with the command?**
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version 2.3.6
Each contig may not represent individual species. Using the genome sequence from single organism as example, a genome of a single organism may not be assembled to chromosomal level in most cases. It will results in large number of contigs due to many reasons such as high repetitive DNA content, low sequencing depth and poor sequence reads quality. The same thing goes to metagenome. DNA that comes from same species in the metagenome may be broken down into several pieces of contigs. There will be also sequencing bias which the DNA from dominated species may be over sequenced.
If you would like to recover the draft genome of novel species or species of interest. I would suggest performing metagenomic binning to taxonomically classify the sequence reads or contigs. Some tools like ClaMS and PhymmBL can achieve such purpose. And you can subsequently fish out the reads from the pool and assemble to a draft assembly. Be aware that to recover a candidate species, you need to have very high sequencing depth to increase the "genome coverage" of the candidate species that you may be interested.
There is one good paper on the classification of metagenomic sequences by Mande et al. (2012). The link is as below: http://bib.oxfordjournals.org/content/13/6/669.long