lastal, there is one version of last-744 came with argpore
ruby
argpore.sh -f test.fa
What ARGpore Does
ARGpore can help users to identify ARG hits on nanopore reads and simultaneously find the carrier population of the identified ARGs by searching against phylogenetic marker genes on nanopore reads
Citation: if you use ARGpore in your nanopore dataset analysis please cite: Xia, Yu, An-Dong Li, Yu Deng, Xiao-Tao Jiang, Li-Guan Li, and Tong Zhang. MinION Nanopore Sequencing Enables Correlation between Resistome Phenotype and Genotype of Coliform Bacteria in Municipal Sewage. Frontiers in Microbiology 2017
ARGpore docs:
ARGpore is designed to predict resistome of 2D.fasta/1D.fasta generated from NanoPore sequencing.
NOTE: You may still use ARGpore for your metagenomic-assembled contig/scaffold, but you would lose bouche of ARGs and taxa due to annotation limitation.
Input:
input of ARGpore is simply your 2D.fasta/1D.fasta
Resistome prediction Algorithm:
STEP1: Your input fasta will be searched against nt-version SARG database (v1.0)
STEP2: Valid alignment (with > 80% similarity over > 70% alignment length by default) will be kept for further filtering of overlap regions
STEP3: If two hit regions on the same read overlaped for > 50% alignment length, only the one with longest ARG hit will be kept,
Taxa Algorithm:
STEP1: Your input fasta will be searched against clade specific marker gene database (MetaPhlan 2)
STEP2: Valid alignment (with > 80% similarity over > 70% alignment length by default) will be kept for taxa annotation
STEP3: Only the best hit with highest bitscore is kept to determine phylogenetic affiliation
Output:
input_runtime_taxa.tab:nanopore reads with valid match to clade specific marker gene
input_runtime_arg.tab:nanopore reads with valid match to SARG database
input_runtime_arg.w.taxa.tab: ARG-containing nanopore reads with taxa annotated