Balík: plasmidid (1.6.5+dfsg-2)

[ Zdroj: plasmidid  ]

mapping-based, assembly-assisted plasmid identification tool

PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification.

PlasmidID is a computational pipeline that maps Illumina reads over plasmid database sequences. The k-mer filtered, most covered sequences are clustered by identity to avoid redundancy and the longest are used as scaffold for plasmid reconstruction. Reads are assembled and annotated by automatic and specific annotation. All information generated from mapping, assembly, annotation and local alignment analyses is gathered and accurately represented in a circular image which allow user to determine plasmidic composition in any bacterial sample.

Ostatné balíky súvisiace s balíkom plasmidid

• dep: bedtools

  suite of utilities for comparing genomic features

• dep: bowtie2

  ultrafast memory-efficient short read aligner

• dep: cd-hit

  suite of programs designed to quickly group sequences

• dep: circos

  plotter for visualizing data

• dep: mash

  fast genome and metagenome distance estimation using MinHash

• dep: ncbi-blast+

  next generation suite of BLAST sequence search tools

• dep: prokka

  rapid annotation of prokaryotic genomes

• dep: python3

  interactive high-level object-oriented language (default python3 version)

• dep: samtools

  processing sequence alignments in SAM, BAM and CRAM formats

• rec: python3-biopython

  Python3 library for bioinformatics

• rec: python3-numpy

  Fast array facility to the Python language (Python 3)

• rec: python3-pandas

  údajové štruktúry „relačných“ dát alebo dát „s označením“

• rec: spades

  genome assembler for single-cell and isolates data sets

• rec: trimmomatic

  flexible read trimming tool for Illumina NGS data

Stiahnuť plasmidid

Stiahnuť pre všetky dostupné architektúry

Architektúra	Veľkosť balíka	Nainštalovaná veľkosť	Súbory
alpha (neoficiálny port)	46.1 kB	331.0 kB	[zoznam súborov]
amd64	46.1 kB	331.0 kB	[zoznam súborov]
arm64	46.1 kB	331.0 kB	[zoznam súborov]
ppc64 (neoficiálny port)	46.1 kB	331.0 kB	[zoznam súborov]