Circlator: automated circularization of genome assemblies using long sequencing reads

[1]  J. Landolin,et al.  Assembling large genomes with single-molecule sequencing and locality-sensitive hashing , 2014, Nature Biotechnology.

[2]  Warren W. Kretzschmar,et al.  Molecular Signatures of Major Depression , 2015, Current Biology.

[3]  N. Loman,et al.  A complete bacterial genome assembled de novo using only nanopore sequencing data , 2015, Nature Methods.

[4]  S. Koren,et al.  One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly. , 2015, Current opinion in microbiology.

[5]  Aaron R. Quinlan,et al.  Poretools: a toolkit for analyzing nanopore sequence data , 2014, bioRxiv.

[6]  Tatiana A. Tatusova,et al.  RefSeq microbial genomes database: new representation and annotation strategy , 2013, Nucleic Acids Res..

[7]  Antonia Furrer,et al.  Handling the 3-methylcytosine lesion by six human DNA polymerases members of the B-, X- and Y-families , 2013, Nucleic acids research.

[8]  Aaron A. Klammer,et al.  Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data , 2013, Nature Methods.

[9]  Alexey A. Gurevich,et al.  QUAST: quality assessment tool for genome assemblies , 2013, Bioinform..

[10]  Heng Li.  Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM , 2013, 1303.3997.

[11]  Matthew Berriman,et al.  BamView: visualizing and interpretation of next-generation sequencing read alignments , 2012, Briefings Bioinform..

[12]  Julian Parkhill,et al.  Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak. , 2012, The New England journal of medicine.

[13]  Daniel J. Wilson,et al.  A pilot study of rapid benchtop sequencing of Staphylococcus aureus and Clostridium difficile for outbreak detection and surveillance , 2012, BMJ Open.

[14]  Sergey I. Nikolenko,et al.  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..

[15]  M. Schatz,et al.  Algorithms Gage: a Critical Evaluation of Genome Assemblies and Assembly Material Supplemental , 2008 .

[16]  Matthew Berriman,et al.  Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data , 2011, Bioinform..

[17]  Miriam L. Land,et al.  Trace: Tennessee Research and Creative Exchange Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification Recommended Citation Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification , 2022 .

[18]  Ning Ma,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

[19]  Steven J. M. Jones,et al.  Circos: an information aesthetic for comparative genomics. , 2009, Genome research.

[20]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[21]  R. Myers,et al.  Mitochondrial involvement in psychiatric disorders , 2008, Annals of medicine.

[22]  Patrick F Chinnery,et al.  Clinical expression of Leber hereditary optic neuropathy is affected by the mitochondrial DNA-haplogroup background. , 2007, American journal of human genetics.

[23]  Mihai Pop,et al.  Minimus: a fast, lightweight genome assembler , 2007, BMC Bioinformatics.

[24]  Yi Xing,et al.  Negative selection pressure against premature protein truncation is reduced by both alternative splicing and diploidy , 2004, Genome Biology.

[25]  S. Cebrat,et al.  Where does bacterial replication start? Rules for predicting the oriC region. , 2004, Nucleic acids research.

[26]  S. Salzberg,et al.  Versatile and open software for comparing large genomes , 2004, Genome Biology.

[27]  Jonathan E. Allen,et al.  Genome sequence of the human malaria parasite Plasmodium falciparum , 2002, Nature.

[28]  S. Dimauro,et al.  Segregation patterns of a novel mutation in the mitochondrial tRNA glutamic acid gene associated with myopathy and diabetes mellitus. , 1995, American journal of human genetics.

[29]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[30]  R. Staden.  A strategy of DNA sequencing employing computer programs. , 1979, Nucleic acids research.