ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers

Direct determination of diploid genome sequences

(2017) Neil I. Weisenfeld et al.   GENOME RESEARCH

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

LRSim: A Linked-Reads Simulator Generating Insights for Better Genome Partitioning

(2017) Ruibang Luo et al.   Computational and Structural Biotechnology Journal

chromPlot: visualization of genomic data in chromosomal context

(2016) Karen Y. Oróstica et al.   BIOINFORMATICS

Genome assembly from synthetic long read clouds

(2016) Volodymyr Kuleshov et al.   BIOINFORMATICS

Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences

(2016) Heng Li   BIOINFORMATICS

Haplotyping germline and cancer genomes with high-throughput linked-read sequencing

(2016) Grace X Y Zheng et al.   NATURE BIOTECHNOLOGY

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

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

(2016) Chen-Shan Chin et al.   NATURE METHODS

Long-read sequence assembly of the gorilla genome

(2016) D. Gordon et al.   SCIENCE

Fast and sensitive taxonomic classification for metagenomics with Kaiju

(2016) Peter Menzel et al.   Nature Communications

CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers

(2015) Rachid Ounit et al.   BMC GENOMICS

Assembling large genomes with single-molecule sequencing and locality-sensitive hashing

(2015) Konstantin Berlin et al.   NATURE BIOTECHNOLOGY

LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads

(2015) René L. Warren et al.   GigaScience

RNA-Skim: a rapid method for RNA-Seq quantification at transcript level

(2014) Zhaojun Zhang et al.   BIOINFORMATICS

In vitro, long-range sequence information for de novo genome assembly via transposase contiguity

(2014) Andrew Adey et al.   GENOME RESEARCH

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH