SLR: a scaffolding algorithm based on long reads and contig classification

Repeat-aware evaluation of scaffolding tools

(2018) Igor Mandric et al.   BIOINFORMATICS

Piercing the dark matter: bioinformatics of long-range sequencing and mapping

(2018) Fritz J. Sedlazeck et al.   NATURE REVIEWS GENETICS

Direct determination of diploid genome sequences

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

Scaffolding and completing genome assemblies in real-time with nanopore sequencing

(2017) Minh Duc Cao et al.   Nature Communications

BOSS: a novel scaffolding algorithm based on an optimized scaffold graph

(2016) Junwei Luo et al.   BIOINFORMATICS

Genome assembly from synthetic long read clouds

(2016) Volodymyr Kuleshov et al.   BIOINFORMATICS

ScaffMatch: scaffolding algorithm based on maximum weight matching

(2015) Igor Mandric et al.   BIOINFORMATICS

Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome

(2015) Sara Goodwin et al.   GENOME RESEARCH

EPGA: de novo assembly using the distributions of reads and insert size

(2014) Junwei Luo et al.   BIOINFORMATICS

SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information

(2014) Marten Boetzer et al.   BMC BIOINFORMATICS

BESST - Efficient scaffolding of large fragmented assemblies

(2014) Kristoffer Sahlin et al.   BMC BIOINFORMATICS

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

(2014) Andrew Adey et al.   GENOME RESEARCH

A comprehensive evaluation of assembly scaffolding tools

(2014) Martin Hunt et al.   GENOME BIOLOGY

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

SCARPA: scaffolding reads with practical algorithms

(2012) N. Donmez et al.   BIOINFORMATICS

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS

BamTools: a C++ API and toolkit for analyzing and managing BAM files

(2011) D. W. Barnett et al.   BIOINFORMATICS

Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences

(2011) Song Gao et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS