Alpha rarefaction using qiime

ShannonBacterial Diversity Index

H =-Σ (PI)

Pi = the proportion of individuals in the I type in the sample. If the total number of individuals in the sample is n and the number of individuals in the I type is Ni, Pi = Ni/N;

The more evenly individual distribution, the greater the H value. If each body belongs to a different type, the diversity index is the largest. If each body belongs to the same type, the diversity index is the smallest.

 

Dominance: Then take two sequences, from the same sample probability Σ (SI (Si-1)/n (N-1 );

 

SimpsonBacterial Diversity Index

The probability of two randomly sampled individuals belongs to different types = 1-the probability of two randomly sampled individuals belongs to the same type; the more even, the greater the value

 

Pd_whole_tree:Pedigree diversity:

Phylogenetic diversity (faith 1992): explores the preservation of evolutionary history, and applies it to populations, communities, geographies, and conservation biology.

Phylobetadiversity (Webb 2002): To explore the distance between communities or indeed lineage and their causes.

Phylogenetic signal and Phylogenetic structure: To explore the coexistence mechanism of community and regional species.

Phylogenetic diversity PD: The sum of the shortest evolutionary branch lengths of all species in a specific location in proportion to the total length of each node Branch (faith, 1992)

Phylogenetic distance: the average value of the length of the lineage branch between the two species in community I and Community II (Webb, 2002)

 

Chao1Species richness index

Schao1 = sobs + N1 (n1-1)/2 (n2 + 1), where schao1 is the estimated out number, sobs is the observed OTU number, n1 indicates the number of out in a single day sequence, and N2 indicates the number of out in a two-day sequence.

 

Observed_speciesOTU count

 

Goods_coverageSequencing depth index

Sequencing depth: c = 1-n1/n. N1 indicates the number of Otus containing only one sequence, and N indicates the total number of sequences in the sample.

 

Qiime computing

16 S building tree:

Align_seq.py: http://qiime.org/scripts/align_seqs.html

Align_seqs.py-I $ PWD/unaligned. FNA-T $ PWD/core_set_aligned.fasta.imputed-o $ PWD/pynast_aligned_defaults/

 

Filter_alignment.py: http://qiime.org/scripts/filter_alignment.html

filter_alignment.py -i seqs_rep_set_aligned.fasta -m lanemask_in_1s_and_0s -o filtered_alignment/

Make_phylogeny.py: http://qiime.org/scripts/make_phylogeny.html

make_phylogeny.py -i $PWD/aligned.fasta -o $PWD/rep_phylo.tre

 

Calculate the Alpha dilution curve:

 

Alpha_rarefaction.py

Http://qiime.org/scripts/alpha_rarefaction.html

alpha_rarefaction.py -i otu_table.biom -o arare_max100/ -t rep_set.tre -m Fasting_Map.txt -e 100

 

-E indicates the depth, which is the same as the-e parameter in Beta diversity.

-- Metrics Shannon, pd_whole_tree, chao1, observed_species, goods_coverage, Simpson

Type to be calculated

 

 

 

Reference: http://blog.sina.com.cn/s/blog_670445240102uw6s.html

Alpha rarefaction using qiime