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In addition, one can generate a taxonomic profile by quantifying the assigned reads, based on read counts or coverage for each individual bin.
However, estimation based on read coverage along the genome suffers from bias due to GC content and other factors.
Contigs from composited metagenomes were binned into metagenome-assembled genomes (MAGs) using MetaBAT (; v. 0.18.6) based on read mapping with Bowtie2.
The method is based on read and verify.
Furthermore, we have a basic algorithm to derive a set of coordinates from DS data based on read counts or sequencing coverage.
Coverage depth statistics were tabulated using in-house PERL scripts and based on read depth values obtained from diBayes output files (*ConsensusCalls.txt).txt
Digital Gene Expression profiling (DGE) was performed based on read abundance and showed that fifteen miRNAs were highly expressed in gastric tissue.
PCR duplicates were identified based on read start and end alignment coordinates.
Scaffolds were formed using the Bambus software [ 98] based on read mate-pairing.
For example, a user can choose to filter variants based on read depth or sequencing quality.
Read coverage was computed and genome annotation was challenged based on read distribution and coverage.
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