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Search results for python genome

708 search results found

Dna Traits ⭐ 64

A fast 23andMe genome text file parser, now superseded by arv

A package for designing compact and comprehensive capture probe sets.

Genomes Pipeline ⭐ 63

MGnify genome analysis pipeline

Tensorflow Neat ⭐ 63

TensorFlow Eager implementation of NEAT and Adaptive HyperNEAT

SV caller for nanopore data

Long Reads Annotation pipeline

Pan Genome Analysis ⭐ 61

Processing pipeline for pan-genome visulization and exploration

Panacota ⭐ 60

PANgenome with Annotations, COre identification, Tree and corresponding Alignments

Toolbox for comparative genomics of MAGs

Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image

Crossmap ⭐ 58

CrossMap is a python program to lift over genome coordinates from one genome version to another.

Phanotate ⭐ 58

PHANOTATE: a tool to annotate phage genomes.

Woltka: a versatile meta'omic data classifier

Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.

Transcriptclean ⭐ 57

Correct mismatches, microindels, and noncanonical splice junctions in long reads that have been mapped to the genome

Assembly Dereplicator ⭐ 57

A tool for removing redundant genomes from a set of assemblies

Primalscheme ⭐ 56

a tool for designing primer panels for multiplex PCR.

Toolbox for including enzyme constraints on a genome-scale model.

Method for detecting STR expansions from short-read sequencing data

Flextaxd ⭐ 54

FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, ganon and more )

⛓ Correct misassemblies using linked AND long reads

Homopolish ⭐ 53

High-quality Nanopore-only genome polisher

Long-read splice alignment with high accuracy

H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)

Genomegtftools ⭐ 52

convert various features into a GFF-like file for use in genome browsers

Semantic Image Manipulation using Scene Graphs (CVPR 2020)

Liftover ⭐ 51

liftover for python, made fast with cython

Coding Genome Reconstruction using Iso-Seq data

Viralmsa ⭐ 50

Reference-guided multiple sequence alignment of viral genomes

Cadd Scripts ⭐ 50

CADD scripts release for offline scoring. For more information about CADD, please visit our website

Nanomonsv ⭐ 50

SV detection tool for nanopore sequence reads

Python package for detection of chimerism and contamination in prokaryotic genomes.

Ranked vaccine peptides for personalized cancer immunotherapy

a collection of scripts for organising bacterial genomes by species

Tools to analyze Dip-C (or other 3C/Hi-C) data

Svim Asm ⭐ 48

Structural Variant Identification Method using Genome Assemblies

A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome

Pyliftover ⭐ 47

Pure-python implementation of UCSC liftOver genome coordinate conversion

Trackhub ⭐ 47

create, manage, and upload track hubs for use in the UCSC genome browser

Pipeline Standardization ⭐ 47

MARVEL: Metagenomic Analyses and Retrieval of Viral ELements

Agfusion ⭐ 46

Python package to annotate and visualize gene fusions.

Prothint ⭐ 45

Protein hint generation pipeline for gene finding in eukaryotic genomes

Easy access to human reference genome sequences

A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing

Long-reads Gap-free Chromosome-scale Assembler

Mtoolbox ⭐ 44

A bioinformatics pipeline to analyze mtDNA from NGS data

Ncov Tools ⭐ 44

Small collection of tools for performing quality control on coronavirus sequencing data and genomes

Quota Alignment ⭐ 44

Guided synteny alignment between duplicated genomes (within specified quota constraint)

Generates an NCBI .tbl file of annotations on a genome.

Tandem Genotypes ⭐ 43

Genomeannotation ⭐ 43

Best practices and workflow for genome annotation

Genome guided re-segmention and visualization for raw nanopore sequencing data.

Millstone ⭐ 43

Genome engineering and analysis software

Metachip ⭐ 42

Horizontal gene transfer (HGT) identification pipeline

Peakachu ⭐ 42

Genome-wide contact analysis using sklearn

Metakallisto ⭐ 42

Using kallisto for metagenomic analysis

Ngs Primerplex ⭐ 42

NGS-PrimerPlex is a high-throughput tool for mupltiplex primer design

Bigg_models ⭐ 41

The BiGG Models website server

Microbeannotator ⭐ 41

Pipeline for metabolic annotation of microbial genomes

Metapalette ⭐ 41

Metagenomic profiling and phylogenetic distances via common kmers

Jgi Query ⭐ 40

A simple command-line tool to download data from Joint Genome Institute databases

Bigslice ⭐ 39

A highly scalable, user-interactive tool for the large scale analysis of Biosynthetic Gene Clusters data

Gtctovcf ⭐ 39

Script to convert GTC/BPM files to VCF

Biopython Coronavirus ⭐ 39

Biopython Jupyter Notebook tutorial to characterize a small genome

August 2019 Consensus Accuracy Update ⭐ 39

A short analysis of Oxford Nanopore consensus accuracy for bacterial genome assemblies

Graph based multi genome aligner

Algorithm For Gene Order Reconstruction in Ancestors

Genomelake ⭐ 37

Simple and efficient access to genomic data for deep learning models.

scripts for estimating bacteria replication rates based on population genome copy number variation

Discosnp ⭐ 35

DiscoSnp is designed for discovering all kinds of SNPs (not only isolated ones), as well as insertions and deletions, from raw set(s) of reads.

Pipeline Nanopore Ref Isoforms ⭐ 35

Pipeline for annotating genomes using long read transcriptomics data with stringtie and other tools

Efficiently keep track of changes to genomes

Xmatchview ⭐ 35

🗻 Visualization of genome/gene sequence synteny

Data_science_in_biology ⭐ 35

projects using galaxy, python, linux command line to analyze sequencing data

Gengraph ⭐ 34

A repository for the GenGraph toolkit for the creation and manipulation of graph genomes

A fast and lightweight python-based linear mixed-model solver for use in genome-wide association studies.

Depth Vrd ⭐ 33

Improving Visual Relation Detection using Depth Maps (ICPR 2020)

Pantagruel ⭐ 32

a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome

Sequencer ⭐ 32

A toolchain of tasks for sequencing and fingerprinting book fulltext

Fast and accurate tool for estimating genomic distances between genome-skims

Mitofinder ⭐ 32

MitoFinder: efficient automated large-scale extraction of mitogenomic data from high throughput sequencing data

Genome-wide reconstruction of complex structural variants

Introgression Detection ⭐ 31

Nano Snakemake ⭐ 31

A snakemake pipeline for SV analysis from nanopore genome sequencing

Charcoal ⭐ 31

Remove contaminated contigs from genomes using k-mers and taxonomies.

all methods related to Enterobase

Fully automated generation of UCSC assembly hubs

Microsatellite Analysis for Normal-Tumor InStability

reference-based long read assemblies of bacterial genomes

Blast Bioinfor Tool ⭐ 30

Python implementation of Basic Local Alignment Search Tool (BLAST) , which is the core algorithm in sequence alignment for genomes.

SQANTI2 is now replaced by SQANTI3. Please go to: https://github.com/ConesaLab/SQANTI3

Treetoreads ⭐ 29

Pipeline to generate NGS reads from a phylogeny

Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity

HMM-based identification and categorization of iron genes and iron gene operons in genomes and metagenomes

A COBRApy extension for genome-scale models of metabolism and expression (ME-models)

Chromatiblock ⭐ 28

Colinear block visualisation tool

Oligominer ⭐ 28

Genome-scale design tool for oligo hybridization probes

Reference_flow ⭐ 28

Reducing reference bias using multiple population reference genomes

VAPiD: Viral Annotation and Identification Pipeline

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