Amplicon sequencing and downstream metagenetic analysis
Often, Illumina amplicon sequencing is used to assess the diversity and composition of microbial populations. For many purposes, the entire downstream bioinformatic analysis may be carried out using only the Qiime pipeline. However, for unusual or very large data, some steps will not work to satisfaction. Hence, alternative bioinformatic programs may have to be found.
This wiki contains a quick overview over the typical steps included in the analysis of amplicon sequencing data. Also, some of the alternative programs are listed, together with reasons to use them, rather than Qiime.
If using Qiime, consult the documentation at http://qiime.org . Qiime is installed on Abel; the default version is v1.5.0, but versions v1.8.0 and v1.9.1 are available as well. Load the default version of Qiime as
Removal of PCR primer sequences
Converting fastq files into fasta files
De-replication of reads
Selecting representative sequences for clusters
Assigning taxonomical identifiers
Analysing OTU tables