plasmid 开源项目推荐（85 个）

Lattice-Automation /seqviz

a JavaScript DNA, RNA, and protein sequence viewer

Binomica-Labs /SpliceCraft

Terminal-based plasmid map viewer, sequence editor, and cloning/mutagenesis workbench in pure Python

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.

clb21565 /mobileOG-db

code repo for mobileOG-db

jvogan /motif

An AI-native molecular biology workbench for Claude Science: Claude opens sequence files and prepares analyses on request; you annotate, align, and review them in an interactive workspace.

BU-ISCIII /plasmidID

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

andrewjpage /tiptoft

Predict plasmids from uncorrected long read data

CCB-SB /plsdb

PLSDB pipeline to collect bacterial plasmids from NCBI

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

DangJem /ggchord

An R package built on ggplot2. Combine independent layers for sequence backbones, interval links, genes, general features, labels and quantitative tracks.

mtisza1 /Cenote-Taker

DEPRECATED: Use Cenote-Taker 3 instead

yqman34 /pl-flow

Synthesize 32 kHz reference-conditioned speech with a two-stage TTS model delivering 83.28 speaker similarity on Seed-TTS-Eval.

octantbio /octopus3

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

mycql /yapv

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

riccabolla /PCNE

Plasmid Copy Number Estimator is a tool to estimate the copy numbers of plasmids detected in an assembled genome