Some tips to optimize bacterial genome assembly
Next-Gen Sequencing
by Stuart Brown
5y ago
I just finished a revised genome assembly for a collaborating lab.  We do de novo sequencing of bacterial genomes all the time, sometimes in batches of 50 or 100 different isolates barcoded together on a high-yield HiSeq run. We typically aim for coverage in the 500x to 1000x range with paired-end 150 base reads. This genome was assembled as part of a "pipeline" script using SPADES, but it did not come out very nicely - over 3000 contigs, most of them small with low coverage.  A FastQC on the raw data looked good (all bases with mean quality  >Q30) except for the last 10 bases show a big d ..read more
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