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Search results for assembly bioinformatics
assembly
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bioinformatics
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86 search results found
Jcvi
⭐
650
Python library to facilitate genome assembly, annotation, and comparative genomics
Nanopolish
⭐
496
Signal-level algorithms for MinION data
Hifiasm
⭐
443
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
Megahit
⭐
442
Ultra-fast and memory-efficient (meta-)genome assembler
Quast
⭐
327
Genome assembly evaluation tool
Pyfastx
⭐
211
a python package for fast random access to sequences from plain and gzipped FASTA/Q files
Masurca
⭐
207
Drep
⭐
199
Rapid comparison and dereplication of genomes
Soapdenovo2
⭐
197
Next generation sequencing reads de novo assembler.
Miniasm
⭐
195
Ultrafast de novo assembly for long noisy reads (though having no consensus step)
Circlator
⭐
193
A tool to circularize genome assemblies
Mag
⭐
164
Assembly and binning of metagenomes
Indra
⭐
154
INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.
Pydna
⭐
140
Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.
Ariba
⭐
135
Antimicrobial Resistance Identification By Assembly
Assemblytics
⭐
124
Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.
Genome_updater
⭐
123
Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy
Redundans
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121
Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.
Bio
⭐
97
Bioinformatics library for .NET
Platon
⭐
93
Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
Assembly Stats
⭐
92
Get assembly statistics from FASTA and FASTQ files
Sigprofilermatrixgenerator
⭐
91
SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file). The tool seamlessly integrates with other SigProfiler tools.
Fermikit
⭐
91
De novo assembly based variant calling pipeline for Illumina short reads
Genefuse
⭐
86
Gene fusion detection and visualization
Arcs
⭐
86
🌈Scaffold genome sequence assemblies using linked or long read sequencing data
Mccortex
⭐
86
De novo genome assembly and multisample variant calling
Flo
⭐
82
Same species annotation lift over pipeline.
Fermi
⭐
68
A WGS de novo assembler based on the FMD-index for large genomes
Aviary
⭐
62
A hybrid assembly and MAG recovery pipeline (and more!)
Tigmint
⭐
53
⛓ Correct misassemblies using linked AND long reads
Unimap
⭐
49
A fork of minimap2 optimized for assembly-to-reference alignment
Appliedgenomics2017
⭐
49
JHU EN.600.649: Computational Genomics: Applied Comparative Genomics
Funcscan
⭐
49
(Meta-)genome screening for functional and natural product gene sequences
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
Dentist
⭐
44
Close assembly gaps using long-reads at high accuracy.
Assembly_improvement
⭐
39
Improve the quality of a denovo assembly by scaffolding and gap filling
Haslr
⭐
39
A fast tool for hybrid genome assembly of long and short reads
Gfapy
⭐
39
Gfapy: a flexible and extensible software library for handling sequence graphs in Python
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).
Mindthegap
⭐
30
MindTheGap is a SV caller for short read sequencing data dedicated to insertion variants (all sizes and types). It can also be used as a local assembly tool.
Transabyss
⭐
30
de novo assembly of RNA-seq data using ABySS
Soapdenovo Trans
⭐
27
SOAPdenovo-Trans, a de novo transcriptome assembler designed specifically for RNA-Seq. We evaluated its performance on transcriptome datasets from rice and mouse.
Teloclip
⭐
26
A tool for the recovery of unassembled telomeres from soft-clipped read alignments.
Awesome Sequencing Tech Papers
⭐
26
A collection of publications on comparison of high-throughput sequencing technologies.
Bioinformatics Course 2020
⭐
23
Socru
⭐
23
Order and orientation of complete bacterial genomes
Metagenomescope
⭐
22
Visualization tool for (meta)genome assembly graphs
Haploclique
⭐
21
Viral quasispecies assembly via maximal clique finding. A method to reconstruct viral haplotypes and detect large insertions and deletions from NGS data.
Elvers
⭐
21
(formerly eelpond) an automated RNA-Seq workflow system
Common_analyses
⭐
20
Repository of common bioinformatics scripts
Scaff10x
⭐
20
Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads
Ntlink
⭐
20
Minimizer-based assembly scaffolding and mapping using long reads
Score Assemblies
⭐
20
Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s)
Hapo G
⭐
18
Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads.
Sigprofilersimulator
⭐
18
SigProfilerSimulator allows realistic simulations of mutational patterns and mutational signatures in cancer genomes. The tool can be used to simulate signatures of single point mutations, double point mutations, and insertion/deletions. Further, the tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
Mof Search
⭐
18
BLAST-like search across all pre-2019 bacteria on ordinary laptop and desktop computers within a few hours
Matam
⭐
18
Mapping-Assisted Targeted-Assembly for Metagenomics
Biosemble
⭐
17
AI assembly of bioNLP wordnets
Bactpipe
⭐
17
BACTpipe: An assembly and annotation pipeline for bacterial genomics
Sigprofilermatrixgeneratorr
⭐
17
R wrapper for utilizing the SigProfilerMatrixGenerator framework
Physlr
⭐
17
⛓️ Construct a Physical Map from Linked Reads
Genome_collector
⭐
17
🌠 Easily download genomes and build BLAST/Bowtie indexes in Python
Genomics_adventure
⭐
17
Workshop on Genomics - Genomics Adventure
Ont Assembly Snake
⭐
16
Snakemake workflow for bacterial genome assembly + polishing for Oxford Nanopore (ONT) sequencing using multiple tools
Pavfinder
⭐
14
🔍 Post Assembly Variants Finder
Bioinformatics Tools
⭐
14
Small and simple scripts useful for various bioinformatics purposes e.g. extract sequences from fasta files
Berokka
⭐
12
🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
Scaffold_builder
⭐
12
Combining de novo and reference-guided assembly with Scaffold_builder
Motifscan
⭐
11
A motif discovery tool to detect the occurrences of known motifs
Polishclr
⭐
10
A nextflow pipeline for polishing CLR assemblies
Bioinformatics Toolbox
⭐
10
Docker container for bioinformatics tools and pipelines
Repp
⭐
10
Repository-based plasmid design
Moclo
⭐
10
Modular cloning simulation with the MoClo framework in Python
Modular Assembly Hs18
⭐
9
Mix and match modular genome assembler components
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
Jasper
⭐
8
This is the official site for JASPER (Jellyfish based Assembly Sequence Polisher for Error Reduction)
Miniphy
⭐
7
Phylogenetic compression of extremely large genome collections [661k ↘𝟏𝟕.𝟓𝐆𝐁, BIGSIdata ↘𝟓𝟐 𝐆𝐁]
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
Cg Pipeline
⭐
6
Genome assembly/prediction/annotation pipeline for the Linux command line
Mikrokondo
⭐
6
A simple pipeline for bacterial assembly and quality control
Kermit
⭐
6
guided genome assembler using colored overlap graphs
Glo
⭐
6
Go Language implementation of LiftOver
Nanoflow
⭐
5
Bioinformatics pipeline for nanopore sequencing data
Appliedgenomics2020
⭐
5
Description Materials for Spring 2020 Applied Genomics Course
Varity
⭐
5
Variant translation library for Clojure
Kcri Cge Bap
⭐
5
KCRI CGE Bacterial Analysis Pipeline
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