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MACVECTOR ASSEMBLE PLASMID INSTALL

from_accession, -a Path to file containing one (plasmid) accession number per line OR list of accession numbers (see -from_command_line).

MACVECTOR ASSEMBLE PLASMID INSTALL

Get the source code from GitHub and, optionally, install HyAsP as a package: Python and the other tools have to be in the PATH or specified through their path options.

Bowtie 2 ( bowtie2 and bowtie2-build version 2.3.3.1).

Trim Galore ( trim_galore, version 0.4.5_dev).

The following requirements have to be satisfied in addition: In order to use HyAsP as part of the provided pipeline starting from FASTQ reads,

BLAST+ ( makeblastdb tblastn and blastn version 2.6.0)īLAST+ is only required for the create command.

Python ( python, version 3.5.4 packages: Bio, math, numpy, os, pandas, random, subprocess, sys).

HyAsP was developed and tested with the following software dependencies: While results/ contains the results of a comparison of HyAsP with plasmidSPAdes, MOB-recon and Recycler.

Using information on the occurrences of known plasmid genes and considering characteristics of the contigs such as read depth and GC content.Ĭitation: Robert Müller, Cedric Chauve "HyAsP, a greedy tool for plasmids identification", Bioinformatics 35(21):4436–4439, Overviewĭirectory HyAsp/ contains the source code of HyAsP, which can be installed as a package through setup.py (see below).ĭirectory databases/ provides exemplary files that can be used to construct a gene database for HyAsP, It combines ideas from both reference-based and depth-based methods to identify plasmids in a greedy algorithm, HyAsP (Hybrid Assember for Plasmids) is a tool for the extracting plasmids from WGS assemblies in an automatic way.