plasmid
There are 35 repositories under plasmid topic.
Lattice-Automation/seqviz
a JavaScript DNA, RNA, and protein sequence viewer
smaegol/PlasFlow
Software for prediction of plasmid sequences in metagenomic assemblies
thanhleviet/ISfinder-sequences
Insertion sequences (Insertion Element) [https://en.wikipedia.org/wiki/Insertion_sequence] collected from ISfinder (https://isfinder.biotoul.fr/)
Shamir-Lab/Recycler
This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye Rozov, Aya Brown Kav, David Bogumil, Naama Shterzer, Eran Halperin, Itzhak Mizrahi, and Ron Shamir
nekokoe/Plasmer
An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features.
andrewjpage/tiptoft
Predict plasmids from uncorrected long read data
BU-ISCIII/plasmidID
PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification.
CCB-SB/plsdb
PLSDB pipeline to collect bacterial plasmids from NCBI
clb21565/mobileOG-db
code repo for mobileOG-db
Lattice-Automation/repp
repository-based plasmid design
leaemiliepradier/PlasForest
A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes
erinyoung/roundabout
Finding regions of similarity between plasmids
mtisza1/Cenote-Taker
DEPRECATED: Use Cenote-Taker 3 instead
mycql/yapv
A library for creating plasmid feature maps with zero external dependencies.
ElianeBriand/plasmid-sketcher
Visual plasmid sketcher
j-w-yun/Plasmid-Planner
Automatically plan the most optimal expression vector using restriction enzymes.
quadram-institute-bioscience/galaxy-tools
A collection of bioinformatics tools for use with galaxy written at Quadram Institute
haradama/pHash
Software to identify known plasmid sequence from metagenomic assembly using Minhash
irahorecka/sequencing-primer-generator
A tool to batch-generate optimal DNA primers for Sanger sequencing. Output .xlsx file is directly compatible with IDT Oligo Entry.
jjti/repp
repository-based plasmid design
monman53/plasmidraw
A simple SVG drawer for plasmid map diagram.
octantbio/octopus3
A method for next-day high-throughput full plasmid sequencing from colonies
plasmid-designer/plasmid-designer
Plasmid Designer and DNA Editor
MaverickTse/FlexiPlasmidDraw
Client-side standalone Plasmid illustration drawing(SVG) for biotech use
th0mr/plasmidcanvas
A simple python plasmid map creator
xiaoli-dong/pathogenseq
Pathogen whole genome sequence (WGS) data analysis pipeline
HHeng-bioinfo/OMAP-KP
Ordered Mapping and Assignment for Plasmid Identification from NGS data for KP
jordanlab/pChunk
Rapid, accurate annotations of Plasmids from Illumina NGS reads
jvrana/reactplasmid
ReactJS library for displaying plasmid maps
cruzryan/gbkToJSON
Converts gbk addgene plasmids to JSON form.
scholl-lab/plasmicheck
Detect and quantify plasmid DNA contamination in sequencing data
angelovangel/nxf-tgs
Process raw Oxford Nanopore data, generate html report, and do de novo assembly (plasmid, amplicon, bacterial genome)
naturepoker/TelePlasmid
A script suite for analyzing protein sequences against NCBI Plasmids database
tiagofilipe12/mash_wrapper
This script runs MASH given a set of reads against specified references.