Dear All
I am currently working on shotgun metagenomics data. I must tell i am very new to this work.
I have PE with 100 bp length from Illumina platform.
My aim in to find the functional annotation and also see differentially expressed bacteria in two groups
The steps i am following are below with some question associated with each step.
1) Trimming with trimmomatic but I read in review Article that LUCY is good for metagenomics data trimming.
Q: Can anyone suggest me if there is metagenomics specific trimming program other than Trimmomatics/Prinseq? What is in general average quality value considered?
2) Metagenome assembly
a) Denovo assembler: MetaVelvet and Meta-IDBA, RAY, SOAP, Celera, Eular ( to compare all)
Q: how to check which assembler is giving better contigs. Is there any tool which checks for output of an assembler?
b) Reference based assembly: MIRA, AMOS, Genometa
Q: I have no idea how it works(on contigs or reads or blast output)? Do we need to blast all the reads with all the bacterial references?
Or these tools have their own reference database? Or to do it with bowtie against the reference? Or if someone have better suggestions?
3) Binning:
a) Sequence similarity based binning: MEGAN, IMG/M , MG-RAST
Q: what is the difference between this and reference based?
b) composition-based binning: GroopM and Concoct, Phylopythia
c) Works on both methods: PhymmB and MetaCluster
Q: suggest what is better tool for binning host associated data?
4) Gene prediction tools: MetaGeneMark and Glimmer-MG,mORFind
Q: suggest what is better tool?
5) Q: How can we do functional annotation?
Cheers,
I am currently working on shotgun metagenomics data. I must tell i am very new to this work.
I have PE with 100 bp length from Illumina platform.
My aim in to find the functional annotation and also see differentially expressed bacteria in two groups
The steps i am following are below with some question associated with each step.
1) Trimming with trimmomatic but I read in review Article that LUCY is good for metagenomics data trimming.
Q: Can anyone suggest me if there is metagenomics specific trimming program other than Trimmomatics/Prinseq? What is in general average quality value considered?
2) Metagenome assembly
a) Denovo assembler: MetaVelvet and Meta-IDBA, RAY, SOAP, Celera, Eular ( to compare all)
Q: how to check which assembler is giving better contigs. Is there any tool which checks for output of an assembler?
b) Reference based assembly: MIRA, AMOS, Genometa
Q: I have no idea how it works(on contigs or reads or blast output)? Do we need to blast all the reads with all the bacterial references?
Or these tools have their own reference database? Or to do it with bowtie against the reference? Or if someone have better suggestions?
3) Binning:
a) Sequence similarity based binning: MEGAN, IMG/M , MG-RAST
Q: what is the difference between this and reference based?
b) composition-based binning: GroopM and Concoct, Phylopythia
c) Works on both methods: PhymmB and MetaCluster
Q: suggest what is better tool for binning host associated data?
4) Gene prediction tools: MetaGeneMark and Glimmer-MG,mORFind
Q: suggest what is better tool?
5) Q: How can we do functional annotation?
Cheers,
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