Genomics/ Sequencing

Question 1

Name the Downstream analysis tools

Answer 1

Kraken, MetaPhlAn2, HUMAnN2, MetaBAT, MetaMLST

Question 2

What analysis tool(s) use compositional analysis

Answer 2

Kraken and MetaPhlAn1

Question 3

What analysis tool(s) use functional analysis

Answer 3

HUMAnN2

Question 4

What analysis tool(s) use genome reconstruction

Answer 4

MetaBAT

Question 5

What analysis tool(s) use strain-level analyis

Answer 5

PanPhlAn and MetaMLST

Question 6

What is Compositional Analysis?

Answer 6

Tells you who is there (i.e. measurement and distribution)

Question 7

What is Functional Analysis?

Answer 7

HUMAnN2 allows you to profile the presence/absence and abundance of microbial pathways in a community (only tells you potential NOT what is actually happening)

Question 8

Describe Kraken

Answer 8

Uses K-mers (random sequences of length K) and stores all possible unique k-mers in a large data base (around 50 GB). It is ultrafast since there is not alignment matching k-mers from input read to k-mer database

Question 9

Describe Metaphlan2

Answer 9

Identifies a unique set of marker genes within a species. It is slower since it requires alignment, but it uses a smaller database

Question 10

Describe MetaBAT

Answer 10

Genome reconstruction

Question 11

What tools are capable of strain-level analysis from shotgun metagenomics?

Answer 11

PanPhlAn, MetaMLST, StrainPhlAn, StrainEst

Question 12

Describe PanPhlAn

Answer 12

Aligns sequencing reads against a species-specific pan-genome database which is constructed from reference genomes.

It predicts which genes are present in the strains from your sample in order to 1) Identify closely related reference strains and 2) Compare strain-level Variation between different samples

Question 13

Describe MetaMLST

Answer 13

Establishes sequence types (STs) by identifying polymorphisms in housekeeping genes.

It does not require prior knowledge on a sample’s microbial composition.

It can simultaneously detect the sequence types (STs) from multiple species

Question 14

Define Meta-transcriptome

Answer 14

The complete collection of a transcribed sequences in a microbial community (protein-coding RNA and non-coding RNA)

Question 15

What can you study with Meta-transcriptomics?

Answer 15

Community functions, responses to different environments, and regulation of gene expression

Question 16

What is the difference between metagenomics and metatranscriptomics

Answer 16

Tells you which genes may be involved, v.s. which genes are actually involved

Question 17

Define OTU

Answer 17

Operational Taxonomic Unit; it is a ‘bin’ that contains sequences/reads that are x% identical to each other

Question 18

Alpha Diversity

Answer 18

Diversity that does not take into account the number of individuals of a species/ measures the diversity within a single sample

Question 19

Beta diversity

Answer 19

Measures diversity between two or more samples

Question 20

Jaccard Similarity

Answer 20

species between both sites / ( #species between both sites + #species unique to the 2nd site #species unique to the 1st site)

Question 21

What is the difference mathmatically between similarity and dissimilarity

Answer 21

Similarity ( is just the equation); dissimilarity is 1- the equation

Question 22

What type of diversity does Jaccard (dis)similarity measure?

Answer 22

Beta Diversity; Measures the presence/absence of species considered (unweighted)

Question 23

What type of diversity does Bray-Curtis (dis)similarity measure?

Answer 23

Beta Diversity; Accounts for the number of times each species is observed (weighted)

Question 24

Bray-Curtis (dis)similarity

Answer 24

(2*sum of the lesser number of individuals for only those species in common between both sites)/ (total number of individuals at site 1 + total number of individuals at site 2)

Question 25

What type of diversity does UniFrac measure?

Answer 25

accounts for phylogeny; allows you to compare communities based on taxonomic distance