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Questions related from Stefano Campanaro
I am comparing variants (mainly SNPs) identified in different S. cerevisiae strains and obtained using different sequencing technologies (i.e. Illumina NextSeq 500 and Proton). I found many...
19 October 2018 496 2 View
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 8,871 2 View
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 8,087 1 View
• From metagenomic analysis nearly complete microbial genomes can be identified. Some of these microbes seem to be unculturable, and are impossible to manage with “standard” microbiological...
18 October 2014 7,815 10 View
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 3,698 4 View
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 2,908 1 View
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 4,334 6 View
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 6,628 7 View
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 3,023 1 View
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 1,466 3 View
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 1,915 3 View
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 605 6 View
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 335 3 View
