Author: Jiao Chen; Jiayu Shang; Jianrong Wang; Yanni Sun
Title: A binning tool to reconstruct viral haplotypes from assembled contigs Document date: 2019_7_16
ID: 2basllfv_48
Snippet: StrainPhlAn (Truong et al., 2017) is also able to to characterize the genetic structure of viral strains in metagenomes. It takes the raw sequencing reads and MetaPhlAn2 (Truong et al., 2015) database of species-specific reference sequences as input and aims to output the most abundant strain for each sample. However, it failed to detect any viral species at the first step running MetaPhlAn2. ConStrains (Luo et al., 2015) is another tool designed.....
Document: StrainPhlAn (Truong et al., 2017) is also able to to characterize the genetic structure of viral strains in metagenomes. It takes the raw sequencing reads and MetaPhlAn2 (Truong et al., 2015) database of species-specific reference sequences as input and aims to output the most abundant strain for each sample. However, it failed to detect any viral species at the first step running MetaPhlAn2. ConStrains (Luo et al., 2015) is another tool designed to identify strain structures from metagenomic data. It uses bowtie2 to map reads to a set of universal genes and infers the within-species strains abundances by utilizing single-nucleotide polymorphism (SNP) patterns. This tool again did not get enough mapped reads to report any strain abundance. And it takes considerable efforts for us to modify their codes for our inputs. Thus, we cannot report the results from StrainPhlAn or ConStrains.
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