Stefano Campanaro

11 Questions 16 Answers 0 Followers

Questions related from Stefano Campanaro

Metagenomics scaffolding: can anyone suggest software to perform this task in an efficient way?

I am checking different software to do the scaffolding of metagenomics assemblies. Despite some assemblers such as metaSPAdes already perform the scaffolding, I would like to verify the...

11 February 2018 8,814 2 View

Can anyone suggest a software to compare microbial genome characteristics?

I am comparing a large number of microbial genomes obtained from a complex microbial community. I performed the main functional annotations for the genes (COG, KEGG, Pfam) and I would perform a...

11 February 2015 8,028 1 View

Which is the best kit (or protocol) to remove ribosomal RNA from total RNA before metatranscriptomic analysis?

We are planning a metatranscriptomic analysis on a microbial community obtained from bioreactors, but we need to remove as much rRNA as possible in order to maximize the number of reads on mRNA....

12 June 2014 3,652 4 View

Has anyone obtained worse assembly results using metavelvet than using velvet?

We are performing trial shotgun assemblies of 80 millions paired-end sequences illumina reads obtained from a bioreactor microbial community. After removing contigs shorter than 1kbp, the assembly...

09 April 2014 2,858 1 View

How can I manage 16S rRNA sequence similar to a species of different phyla?

I am checking some ribotypes obtained using 16S high-throughput sequencing (V4 region) of a microbial community. I have found a ribotype (obtained from clustering of sequences at 97% similarity)...

09 April 2014 4,287 6 View

Can someone suggest primers for 16S rDNA genes matching both Archea and Bacteria?

I am planning analysis on a complex microbial community containing high number of species of bacteria and archaea using 16 rDNA sequencing. On previous experiments I have used two different...

08 February 2014 6,578 7 View

Which is the best tool for operon prediction in bacteria?

I am analyzing a bacterial genome recently sequenced in our group. After gene finding and annotation I would have a rough overview of its operon structure using a bioinformatic software. Can...

27 September 2013 2,977 1 View

Assembly of metagenomics shotgun sequences obtained with the Proton sequencer

Does someone have assembled short reads obtained from shotgun sequencing (Proton sequencer) of complex microbial communities? Which is the best tool for assembly of these reads (not-paired-end)?...

15 September 2013 1,404 3 View

Can anyone suggest a kit or a protocol for RNA isolation from slugde samples?

I am planning a metatranscriptomic experiment on sludge samples. I have extracted RNA from a number of different bacteria but I have never performed metatranscriptomic analysis in the past. Does...

29 August 2013 1,856 3 View

Velvet/Abyss assembly of Illumina sequences. Is it possible to obtain quality files for the final assembly?

I am assembling Illumina sequences (MySEQ paired end 250+250 bases) obtained for bacterial genomes. I used both Velvet and Abyss software but I did not obtained a quality files for the genome...

25 June 2013 553 6 View

Software for genomes alignment

Which is the best software to perform full genome alignments of strictly related species or strains and identify SNPs and InDels taking into account also the quality of the genome at every...

29 September 2012 290 3 View