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Questions related from Stefano Campanaro
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 8,799 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 8,019 1 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 3,642 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 2,848 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 4,279 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 6,567 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 2,967 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 1,393 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 544 6 View