Lattice-Automation/seqviz

a JavaScript DNA, RNA, and protein sequence viewer

Language: TypeScript - Size: 112 MB - Last synced: 12 days ago - Pushed: about 1 month ago - Stars: 213 - Forks: 48

xiaoli-dong/pathogenseq

Pathogen whole genome sequence (WGS) data analysis pipeline

Language: Nextflow - Size: 2.47 MB - Last synced: 15 days ago - Pushed: 15 days ago - Stars: 2 - Forks: 1

th0mr/plasmidcanvas

A simple python plasmid map creator

Language: Python - Size: 5.2 MB - Last synced: 19 days ago - Pushed: 19 days ago - Stars: 1 - Forks: 0

smaegol/PlasFlow

Software for prediction of plasmid sequences in metagenomic assemblies

Language: Python - Size: 37.7 MB - Last synced: 18 days ago - Pushed: almost 3 years ago - Stars: 89 - Forks: 27

CCB-SB/plsdb

PLSDB pipeline to collect bacterial plasmids from NCBI

Language: Python - Size: 1.06 MB - Last synced: 3 days ago - Pushed: 6 months ago - Stars: 31 - Forks: 4

j-w-yun/Plasmid-Planner

Automatically plan the most optimal expression vector using restriction enzymes.

Language: Java - Size: 861 KB - Last synced: 3 months ago - Pushed: over 6 years ago - Stars: 4 - Forks: 1

jjti/repp

repository-based plasmid design

Language: Go - Size: 338 MB - Last synced: 4 months ago - Pushed: over 1 year ago - Stars: 2 - Forks: 5

mtisza1/Cenote-Taker

DEPRECATED: Use Cenote-Taker 3 instead

Language: Shell - Size: 147 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 14 - Forks: 2

quadram-institute-bioscience/galaxy-tools

A collection of bioinformatics tools for use with galaxy written at Quadram Institute

Language: HTML - Size: 295 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 4 - Forks: 3

andrewjpage/tiptoft

Predict plasmids from uncorrected long read data

Language: Python - Size: 37.8 MB - Last synced: 20 days ago - Pushed: over 4 years ago - Stars: 37 - Forks: 10

clb21565/mobileOG-db

code repo for mobileOG-db

Language: Python - Size: 162 KB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 15 - Forks: 4

jordanlab/pChunk

Rapid, accurate annotations of Plasmids from Illumina NGS reads

Language: R - Size: 12.7 KB - Last synced: 7 months ago - Pushed: over 4 years ago - Stars: 1 - Forks: 0

leaemiliepradier/PlasForest

A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes

Language: Python - Size: 89.6 MB - Last synced: 7 months ago - Pushed: about 1 year ago - Stars: 13 - Forks: 6

monman53/plasmidraw

A simple SVG drawer for plasmid map diagram.

Language: JavaScript - Size: 84 KB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 3 - Forks: 0

thanhleviet/ISfinder-sequences

Insertion sequences (Insertion Element) [https://en.wikipedia.org/wiki/Insertion_sequence] collected from ISfinder (https://isfinder.biotoul.fr/)

Size: 3.77 MB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 53 - Forks: 11

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

Language: Python - Size: 7.34 MB - Last synced: 7 months ago - Pushed: about 3 years ago - Stars: 53 - Forks: 7

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.

Language: Python - Size: 63.5 KB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 2 - Forks: 0

cruzryan/gbkToJSON

Converts gbk addgene plasmids to JSON form.

Language: Go - Size: 17.6 KB - Last synced: 10 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

octantbio/octopus3

A method for next-day high-throughput full plasmid sequencing from colonies

Language: Python - Size: 173 MB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 1 - Forks: 0

Lattice-Automation/repp Fork of jjti/repp

repository-based plasmid design

Language: Go - Size: 339 MB - Last synced: 10 months ago - Pushed: over 1 year ago - Stars: 22 - Forks: 4

erinyoung/roundabout

Finding regions of similarity between plasmids

Language: Nextflow - Size: 1.15 MB - Last synced: 10 months ago - Pushed: over 1 year ago - Stars: 5 - Forks: 0

nekokoe/Plasmer

An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features.

Language: Perl - Size: 128 KB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 5 - Forks: 1

BU-ISCIII/plasmidID

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

Language: Shell - Size: 91.8 MB - Last synced: 7 months ago - Pushed: almost 3 years ago - Stars: 35 - Forks: 8

plasmid-designer/plasmid-designer

Plasmid Designer and DNA Editor

Language: TypeScript - Size: 2.83 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 2 - Forks: 1

mycql/yapv

A library for creating plasmid feature maps with zero external dependencies.

Language: TypeScript - Size: 1.77 MB - Last synced: 11 days ago - Pushed: over 1 year ago - Stars: 5 - Forks: 0

haradama/pHash

Software to identify known plasmid sequence from metagenomic assembly using Minhash

Language: Go - Size: 15.9 MB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 3 - Forks: 0

jvrana/reactplasmid

ReactJS library for displaying plasmid maps

Language: JavaScript - Size: 739 KB - Last synced: 4 months ago - Pushed: about 6 years ago - Stars: 1 - Forks: 0

naturepoker/TelePlasmid

A script suite for analyzing protein sequences against NCBI Plasmids database

Language: Shell - Size: 80.8 MB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

ElianeBriand/plasmid-sketcher Fork of vixis/angularplasmid

Visual plasmid sketcher

Language: JavaScript - Size: 3.06 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 4 - Forks: 1

AlexOrlek/MOBtyping

Language: Python - Size: 4.14 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 1 - Forks: 0

MaverickTse/FlexiPlasmidDraw

Client-side standalone Plasmid illustration drawing(SVG) for biotech use

Language: JavaScript - Size: 436 KB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 2 - Forks: 1

BU-ISCIII/plasmidID_test

is an open source software that implements a new method for plasmid identification, annotation and representation. It uses a mapping approach to determine the most likely plasmids present in a sample, genes are annotated and blast algorithm is used to locate AB-resistance genes, replisomes and insertion sequences present in those plasmids. The final output is the representation of those elements in a circular drawing adapted to plasmid configuration.

Language: Shell - Size: 59 MB - Last synced: about 1 year ago - Pushed: almost 6 years ago - Stars: 2 - Forks: 0

tiagofilipe12/mash_wrapper

This script runs MASH given a set of reads against specified references.

Language: Python - Size: 54.7 KB - Last synced: 29 days ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0