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Search results for pipeline assembly
assembly
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pipeline
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73 search results found
Squeezemeta
⭐
308
A complete pipeline for metagenomic analysis
Purge_dups
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178
haplotypic duplication identification tool
3d Dna
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176
3D de novo assembly (3D DNA) pipeline
Mag
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164
Assembly and binning of metagenomes
Vgp Assembly
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160
VGP repository for the genome assembly working group
Redundans
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121
Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.
Shovill
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104
⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads
Webrisc V
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102
WebRISC-V: A Web-Based Education-Oriented RISC-V Pipeline Simulation Environment [PHP]
Fungap
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102
FunGAP: fungal Genome Annotation Pipeline
Viralrecon
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101
Assembly and intrahost/low-frequency variant calling for viral samples
Emg Viral Pipeline
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98
VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
Fermikit
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91
De novo assembly based variant calling pipeline for Illumina short reads
Arcs
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86
🌈Scaffold genome sequence assemblies using linked or long read sequencing data
Ont Assembly Polish
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82
ONT assembly and Illumina polishing pipeline
Nes Pipeline
⭐
80
🔄 Continuous integration for NES homebrew that adds screenshots taken in the cloud.
Aviary
⭐
62
A hybrid assembly and MAG recovery pipeline (and more!)
Helix Publishing Pipeline
⭐
57
Unified publishing for Sitecore Helix solutions that extends existing Visual Studio and command line workflows
Muffin
⭐
56
hybrid assembly and differential binning workflow for metagenomics, transcriptomics and pathway analysis
Falcon Phase
⭐
53
FALCON-Phase integrates PacBio long-read assemblies with Phase Genomics Hi-C data to create phased, diploid, chromosome-scale scaffolds
Rapt
⭐
51
Read Assembly and Annotation Pipeline Tool
Funcscan
⭐
49
(Meta-)genome screening for functional and natural product gene sequences
Bacass
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47
Simple bacterial assembly and annotation pipeline
Asap
⭐
46
A scalable bacterial genome assembly, annotation and analysis pipeline
Microbiomebestpracticereview
⭐
45
Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
Vsts Assemblyinfo Task
⭐
40
Assembly Info is an extension for Azure DevOps that populates assembly information metadata from a build pipeline.
Dnapipete
⭐
38
dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs in newly sequenced genomes since it does not require genome assembly and works on small datasets (< 1X).
Nanopore Paper Analysis
⭐
30
Code for nanopore paper
Rampart
⭐
27
A configurable de novo assembly pipeline
Sars Cov 2
⭐
23
SARS-CoV-2 variant calling and consensus assembly pipeline
Gatb Minia Pipeline
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22
GATB Minia assembly pipeline
Nanoflow
⭐
20
🔬 De novo assembly of nanopore reads using nextflow
Bactpipe
⭐
17
BACTpipe: An assembly and annotation pipeline for bacterial genomics
Tracespipe
⭐
16
Reconstruction and analysis of viral and host genomes at multi-organ level
Metavic
⭐
15
Virus metagenomic pipeline for unknown host or in absence of a host genome
Asset
⭐
15
assembly evaluation tool
Poretally
⭐
15
Benchmark MinION assembler pipelines and publish your results in a heartbeat!
Eukrhythmic
⭐
14
A metatranscriptomic pipeline optimized for the study of microeukaryotes.
De Novo Transcriptome Assembly Pipeline
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13
Combined de novo transcriptome assembly - multiple assemblers - multiple parameters
Dib Mmetsp
⭐
12
Code to generate re-assemblies of the Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP)
Bohra
⭐
12
A pipeline for bioinformatics analysis of bacterial genomes
Kite
⭐
12
Kite: Architecture Simulator for RISC-V Instruction Set
Minys
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11
MineYourSymbiont : Targetted genome assembly for metagenomics pipeline.
Genomeannotator
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11
Pipeline for the identification of (coding) gene structures in draft genomes.
Clin Mngs
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10
Clin-mNGS: Automated pipeline for pathogen detection from clinical metagenomic data
Polishclr
⭐
10
A nextflow pipeline for polishing CLR assemblies
Irys Scaffolding
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10
scripts to parse IrysView output
Banzai Microbialgenomics Pipeline
⭐
10
Banzai is a Microbial Genomics Next Generation Sequencing (NGS) Pipeline Tool developed within Dr Scott Beatson’s Group at the University of Queensland
Datapipe
⭐
10
A data processing framework
Vipr
⭐
10
Assembly and intrahost / low-frequency variant calling for viral samples
Pirate
⭐
10
PiRATE (Pipeline to Retrieve and Annotate Transposable Elements)
Prymetime
⭐
10
Pipeline for Recombinant Yeast genoMEs That Identifies Markers of Engineering
Amos
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10
A clone of the official AMOS git repo on sourceforge: https://sourceforge.net/projects/amos/
Arks
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9
🌈Alignment-free scaffolding of genome assemblies with 10x Genomics Chromium reads
Modular Assembly Hs18
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9
Mix and match modular genome assembler components
Pathogendb Pipeline
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9
Pipeline for genome assembly + annotation for pathogen surveillance
Nextflow Tychus
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9
Hyasp
⭐
8
Hybrid Assembler for Plasmids
Viral Assemble
⭐
8
viral-ngs: genome assembly and scaffolding
Nougat
⭐
8
Project Diploid Assembly
⭐
8
Pipeline code for creating a fully haplotype-resolved assembly from a combination of PacBio/ONT long reads and Illumina Strand-seq data
Hic Pipeline
⭐
8
A pipeline for scaffolding a genome assembly using Hi-C
Metassemble
⭐
7
Scripts to run several metagenomics assembly programs
Scanpav
⭐
7
Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.
Scaffhic
⭐
7
Pipeline for genome scaffolding by modelling distributions of HiC pairs
Pipeline Assembly
⭐
7
Assembly for the DAISY Pipeline 2 distribution
Mag_snakemake_wf
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7
Recovery of prokaryotic genomes from shotgun metagenomic sequencing data
Seqcap_pop
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6
A pipeline for de novo assembly of population-level sequence capture datasets.
Superplus
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6
Cg Pipeline
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6
Genome assembly/prediction/annotation pipeline for the Linux command line
Mikrokondo
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6
A simple pipeline for bacterial assembly and quality control
Matafiler
⭐
5
Metagenomic assembly, genome reconstruction and functional as well as taxonomic profiling
Spoonfednanopore
⭐
5
The world's simplest open-source nanopore alignment and assembly algorithm
Kcri Cge Bap
⭐
5
KCRI CGE Bacterial Analysis Pipeline
Pipeline
⭐
5
Create assembly lines in Clojure.
Plasmident
⭐
5
Pipeline for identification of circular plasmids from genome assemblies and resistance gene annotation
Gametebinning
⭐
5
Mugqic_pipelines
⭐
5
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