MeDuSa: a multi-draft based scaffolder

Ragout--a reference-assisted assembly tool for bacterial genomes

(2014) M. Kolmogorov et al.   BIOINFORMATICS

Draft genomes of three Antarctic Psychrobacter strains producing antimicrobial compounds against Burkholderia cepacia complex, opportunistic human pathogens

(2014) Marco Fondi et al.   Marine Genomics

The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification

(2014) T.B.K. Reddy et al.   NUCLEIC ACIDS RESEARCH

A comprehensive evaluation of assembly scaffolding tools

(2014) Martin Hunt et al.   GENOME BIOLOGY

FPSAC: fast phylogenetic scaffolding of ancient contigs

(2013) Ashok Rajaraman et al.   BIOINFORMATICS

Reference-assisted chromosome assembly

(2013) J. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies

(2012) A. A. Gritsenko et al.   BIOINFORMATICS

SCARPA: scaffolding reads with practical algorithms

(2012) N. Donmez et al.   BIOINFORMATICS

Fast scaffolding with small independent mixed integer programs

(2011) L. Salmela et al.   BIOINFORMATICS

GAGE: A critical evaluation of genome assemblies and assembly algorithms

(2011) S. L. Salzberg et al.   GENOME RESEARCH

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

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

Phylogenetic comparative assembly

(2010) Peter Husemann et al.   Algorithms for Molecular Biology

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

(2010) Murray P Cox et al.   BMC BIOINFORMATICS

SOPRA: Scaffolding algorithm for paired reads via statistical optimization

(2010) Adel Dayarian et al.   BMC BIOINFORMATICS

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

ABySS: A parallel assembler for short read sequence data

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

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Algorithm of OMA for large-scale orthology inference

(2008) Alexander CJ Roth et al.   BMC BIOINFORMATICS