Recent advances in sequence assembly: principles and applications (Q38814575)

6 September 2017

title

Recent advances in sequence assembly: principles and applications (English)

1 reference

6 September 2017

Yi-Ping Phoebe Chen

6

0 references

author name string

Qingfeng Chen

1

1 reference

6 September 2017

Chaowang Lan

2

1 reference

6 September 2017

Liang Zhao

3

1 reference

6 September 2017

Jianxin Wang

4

1 reference

6 September 2017

Baoshan Chen

5

1 reference

6 September 2017

publication date

26 April 2017

1 reference

Briefings in functional genomics

6 September 2017

published in

1 reference

Assembly algorithms for next-generation sequencing data

6 September 2017

cites work

1 reference

Next-generation sequence assembly: four stages of data processing and computational challenges

21 January 2018

1 reference

Computer programs for the assembly of DNA sequences

21 January 2018

1 reference

Succinct data structures for assembling large genomes

21 January 2018

1 reference

Bambus 2: scaffolding metagenomes

21 January 2018

1 reference

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

21 January 2018

1 reference

Meta-IDBA: a de Novo assembler for metagenomic data

21 January 2018

1 reference

Full-length transcriptome assembly from RNA-Seq data without a reference genome

21 January 2018

1 reference

De novo assembly and analysis of RNA-seq data.

21 January 2018

1 reference

Hybrid error correction and de novo assembly of single-molecule sequencing reads

21 January 2018

1 reference

Pathset graphs: a novel approach for comprehensive utilization of paired reads in genome assembly

21 January 2018

1 reference

A new algorithm for DNA sequence assembly

21 January 2018

1 reference

An Eulerian path approach to DNA fragment assembly

21 January 2018

1 reference

Bioinformatics challenges of new sequencing technology

21 January 2018

1 reference

Genome assembly reborn: recent computational challenges

21 January 2018

1 reference

Targeted chromosomal duplications and inversions in the human genome using zinc finger nucleases

21 January 2018

1 reference

Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls

21 January 2018

1 reference

Integrating common and rare genetic variation in diverse human populations

21 January 2018

1 reference

Understanding alternative splicing: towards a cellular code

21 January 2018

1 reference

Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut.

21 January 2018

1 reference

A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers

21 January 2018

1 reference

Extending assembly of short DNA sequences to handle error.

21 January 2018

1 reference

SEQAID: a DNA sequence assembling program based on a mathematical model

21 January 2018

1 reference

Short read fragment assembly of bacterial genomes

21 January 2018

1 reference

ALLPATHS: de novo assembly of whole-genome shotgun microreads

21 January 2018

1 reference

Velvet: algorithms for de novo short read assembly using de Bruijn graphs

21 January 2018

1 reference

ABySS: a parallel assembler for short read sequence data

21 January 2018

1 reference

SOAP3-dp: fast, accurate and sensitive GPU-based short read aligner

21 January 2018

1 reference

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads.

21 January 2018

1 reference

Performance comparison of benchtop high-throughput sequencing platforms

21 January 2018

1 reference

Sense from sequence reads: methods for alignment and assembly

21 January 2018

1 reference

Whole-genome sequence assembly for mammalian genomes: Arachne 2.

21 January 2018

1 reference

A whole-genome assembly of Drosophila

21 January 2018

1 reference

How to apply de Bruijn graphs to genome assembly

21 January 2018

1 reference

Using the Acropora digitifera genome to understand coral responses to environmental change

21 January 2018

1 reference

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

21 January 2018

1 reference

Sequence assembly demystified

21 January 2018

1 reference

Quake: quality-aware detection and correction of sequencing errors

21 January 2018

1 reference

Functional metagenomic profiling of nine biomes

21 January 2018

1 reference

Metagenomic discovery of biomass-degrading genes and genomes from cow rumen

21 January 2018

1 reference

Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads

21 January 2018

1 reference

Fast and accurate short read alignment with Burrows-Wheeler transform

21 January 2018

1 reference

SOAP: short oligonucleotide alignment program

21 January 2018

1 reference

Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms

21 January 2018

1 reference

Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications

21 January 2018

1 reference

A framework for variation discovery and genotyping using next-generation DNA sequencing data

21 January 2018

1 reference

Mapping short DNA sequencing reads and calling variants using mapping quality scores

21 January 2018

1 reference

Dindel: accurate indel calls from short-read data

21 January 2018

1 reference

Uncertainty in homology inferences: assessing and improving genomic sequence alignment

21 January 2018

1 reference

SNP detection for massively parallel whole-genome resequencing

21 January 2018

1 reference

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

21 January 2018

1 reference

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

21 January 2018

1 reference

Fast gapped-read alignment with Bowtie 2

21 January 2018

1 reference

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

21 January 2018

1 reference

Comparative genome assembly

21 January 2018

1 reference

An improved algorithm for matching biological sequences.

21 January 2018

1 reference

Efficient construction of an assembly string graph using the FM-index

21 January 2018

1 reference

Efficient de novo assembly of large genomes using compressed data structures

21 January 2018

1 reference

Long-read sequence assembly of the gorilla genome

21 January 2018

1 reference

Informed and automated k-mer size selection for genome assembly

21 January 2018

1 reference

DSK: k-mer counting with very low memory usage

21 January 2018

1 reference

Assembling millions of short DNA sequences using SSAKE.

21 January 2018

1 reference

Assembler for de novo assembly of large genomes

21 January 2018

1 reference

SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing

21 January 2018

1 reference

QSRA: a quality-value guided de novo short read assembler

21 January 2018

1 reference

Computational complexity of multiple sequence alignment with SP-score

21 January 2018

1 reference

Assemblathon 1: a competitive assessment of de novo short read assembly methods

21 January 2018

1 reference

De novo genome assembly: what every biologist should know

21 January 2018

1 reference

Next-generation sequencing platforms

21 January 2018

1 reference

Field guide to next‐generation DNA sequencers

21 January 2018

1 reference

Error filtering, pair assembly and error correction for next-generation sequencing reads

21 January 2018

1 reference

Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform.

21 January 2018

1 reference

Ironing out the wrinkles in the rare biosphere through improved OTU clustering

21 January 2018

1 reference

PEAR: a fast and accurate Illumina Paired-End reAd mergeR.

21 January 2018

1 reference

COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly

21 January 2018

1 reference

BLESS: bloom filter-based error correction solution for high-throughput sequencing reads.

21 January 2018

1 reference

PANDAseq: paired-end assembler for illumina sequences

21 January 2018

1 reference

Removing noise from pyrosequenced amplicons

21 January 2018

1 reference

Accurate determination of microbial diversity from 454 pyrosequencing data

21 January 2018

1 reference

A survey of error-correction methods for next-generation sequencing

21 January 2018

1 reference

Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data

21 January 2018

1 reference

HiTEC: accurate error correction in high-throughput sequencing data

21 January 2018

1 reference

ECHO: a reference-free short-read error correction algorithm

21 January 2018

1 reference

Automated finishing with autofinish

21 January 2018

1 reference

A de novo metagenomic assembly program for shotgun DNA reads.

21 January 2018

1 reference

Genomic mapping by fingerprinting random clones: a mathematical analysis

21 January 2018

1 reference

A view of cloud computing

21 January 2018

1 reference

SparkSeq: fast, scalable and cloud-ready tool for the interactive genomic data analysis with nucleotide precision

21 January 2018

1 reference

Parallel mutual information estimation for inferring gene regulatory networks on GPUs

21 January 2018

1 reference

Real-time DNA sequencing from single polymerase molecules

21 January 2018

1 reference

A window into third-generation sequencing

21 January 2018

1 reference

Virtual terminator nucleotides for next-generation DNA sequencing.

21 January 2018

1 reference

Nanopore Sequencing: Electrical Measurements of the Code of Life

21 January 2018

1 reference

Faster sequencers, larger datasets, new challenges

21 January 2018

1 reference

DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies

21 January 2018

1 reference

Phased diploid genome assembly with single-molecule real-time sequencing.

21 January 2018

1 reference

PacBio Sequencing and Its Applications

21 January 2018

1 reference

Illumina Synthetic Long Read Sequencing Allows Recovery of Missing Sequences even in the "Finished" C. elegans Genome

21 January 2018

1 reference

Reducing assembly complexity of microbial genomes with single-molecule sequencing

21 January 2018

1 reference

An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data

21 January 2018

1 reference

Evaluation and Validation of Assembling Corrected PacBio Long Reads for Microbial Genome Completion via Hybrid Approaches

21 January 2018

1 reference

The advent of personal genome sequencing

21 January 2018

1 reference

Detection of mixed infection from bacterial whole genome sequence data allows assessment of its role in Clostridium difficile transmission

21 January 2018

1 reference

Proportioning whole-genome single-nucleotide-polymorphism diversity for the identification of geographic population structure and genetic ancestry

21 January 2018

1 reference

SNP discovery and linkage map construction in cultivated tomato.

21 January 2018

1 reference

Sequencing of natural strains of Arabidopsis thaliana with short reads

21 January 2018

1 reference

Predicting single nucleotide polymorphisms (SNP) from DNA sequence by support vector machine

21 January 2018

1 reference

Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly

21 January 2018

1 reference

Size does matter: Application-driven approaches for soil metagenomics

21 January 2018

1 reference

The effect of sequencing errors on metagenomic gene prediction

21 January 2018

1 reference

A human gut microbial gene catalogue established by metagenomic sequencing

21 January 2018

1 reference

Ray Meta: scalable de novo metagenome assembly and profiling.

21 January 2018

1 reference

De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities

21 January 2018

1 reference

21 January 2018

Identifiers

DOI

10.1093/BFGP/ELX006

1 reference

6 September 2017

1 reference