{"id":15315,"date":"2017-10-16T12:00:19","date_gmt":"2017-10-16T11:00:19","guid":{"rendered":"https:\/\/blogs.nature.com\/naturejobs\/?p=15315"},"modified":"2017-10-21T17:38:02","modified_gmt":"2017-10-21T16:38:02","slug":"techblog-the-nanopore-toolbox","status":"publish","type":"post","link":"https:\/\/blogs.nature.com\/naturejobs\/2017\/10\/16\/techblog-the-nanopore-toolbox\/","title":{"rendered":"TechBlog: The nanopore toolbox"},"content":{"rendered":"
\"550285a-i2\"<\/a>

{credit}Nik Spencer\/Nature{\/credit}<\/p><\/div>\n

For this week’s Technology Feature, Michael Eisenstein wrote about the technology, applications, and challenges of nanopore DNA sequencing<\/a>. In brief, the technology involves threading intact pieces of DNA through a\u00a0tiny aperture in a membrane or other barrier,\u00a0through which a current flows. As each base passes,\u00a0it disrupts that current in a characteristic way, allowing specialized software to determine the sequence.<\/p>\n

The technology\u00a0has multiple benefits: it’s relatively inexpensive and compact, and produces exceptionally long reads. But the\u00a0resulting\u00a0error rate is also higher than some other technologies. What that means is, informatics\u00a0tools designed to handle short-read data can often stumble when confronted with nanopore sequences. But a growing collection of dedicated long-read tools is rapidly filling in the gap. I asked a few nanopore veterans to help me compile a list.<\/p>\n

<\/p>\n

Real-time data analysis<\/strong><\/p>\n

MinoTour —\u00a0https:\/\/minotour.nottingham.ac.uk\/<\/a><\/p>\n

Basecallers<\/strong><\/p>\n

Albacore —\u00a0https:\/\/nanoporetech.com<\/a>
\nChiron —\u00a0https:\/\/github.com\/haotianteng\/chiron<\/a>
\nScrappie —\u00a0https:\/\/github.com\/nanoporetech\/scrappie<\/a><\/p>\n

(Ryan R. Wick, Louise Judd, and Kathryn Holt at the University of Melbourne, Australia, recently performed a comprehensive comparison of nanopore basecallers. You can read their analysis here<\/a>.)<\/p>\n

Data Extraction<\/strong><\/p>\n

poRe — https:\/\/sourceforge.net\/projects\/rpore\/<\/a>
\nPoretools — https:\/\/github.com\/arq5x\/poretools<\/a><\/p>\n

QC\/Trimming<\/strong><\/p>\n

Porechop — https:\/\/github.com\/rrwick\/Porechop<\/a>
\nNanoOK — https:\/\/documentation.tgac.ac.uk\/display\/NANOOK\/<\/a>
\nPicopore — https:\/\/github.com\/scottgigante\/picopore<\/a><\/p>\n

Sequence Alignment<\/strong><\/p>\n

GraphMap — https:\/\/github.com\/isovic\/graphmap<\/a>
\nLAST — https:\/\/last.cbrc.jp\/<\/a>
\nMarginAlign — https:\/\/github.com\/benedictpaten\/marginAlign<\/a>
\nMiniMap2 — https:\/\/github.com\/lh3\/minimap2<\/a><\/p>\n

Variant Detection (SNPs and SVs)<\/strong><\/p>\n

Nanopolish — https:\/\/github.com\/jts\/nanopolish<\/a>
\nNanoSV — https:\/\/github.com\/mroosmalen\/nanosv<\/a>
\nSniffles — https:\/\/github.com\/fritzsedlazeck\/Sniffles\/wiki<\/a><\/p>\n

Long-read Assembly<\/strong><\/p>\n

Canu — https:\/\/github.com\/marbl\/canu<\/a>
\nMECAT —\u00a0https:\/\/github.com\/xiaochuanle\/MECAT<\/a>
\nMiniasm — https:\/\/github.com\/lh3\/miniasm<\/a><\/p>\n

Hybrid (Short + Long-read) Assembly<\/strong><\/p>\n

MaSuRCA — https:\/\/www.genome.umd.edu\/masurca.html<\/a>
\nSPAdes — https:\/\/bioinf.spbau.ru\/spades<\/a>
\nUnicycler — https:\/\/github.com\/rrwick\/Unicycler<\/a><\/p>\n

Assembly Polishing<\/strong><\/p>\n

Racon — https:\/\/github.com\/isovic\/racon<\/a>
\nNanopolish — https:\/\/github.com\/jts\/nanopolish<\/a><\/p>\n

Methylation Detection<\/strong><\/p>\n

Nanopolish — https:\/\/github.com\/jts\/nanopolish<\/a>
\nNanoraw —\u00a0https:\/\/nanoraw.readthedocs.io\/<\/a>
\nSignalAlign — https:\/\/github.com\/ArtRand\/signalAlign<\/a><\/p>\n

Putting it all together…<\/strong><\/p>\n

For a\u00a0sense of how some of these pieces fit together and integrate with other (non-nanopore-specific) tools, check out Nicholas Loman’s pipeline for viral consensus genome sequence analysis<\/a>, published in May in Nature Protocols<\/em>. See also PoreCamp<\/a>, a\u00a0“training bootcamp” for the MinION, and a recent review in Genome Biology<\/em><\/a>.<\/p>\n

h\/t Miten Jain, Nicholas Loman, Benedict Paten, Adam Phillippy, Keith Robison, Mick Watson<\/i><\/p>\n

Jeffrey Perkel<\/strong> is Technology Editor,<\/em> Nature<\/p>\n

 <\/p>\n

Suggested posts<\/strong><\/p>\n

Jupyter powers bioinformatics, again<\/a><\/p>\n

Mike Goodstadt: A circuitous route to bioinformatics<\/a><\/p>\n

Jupyter joins the Galaxy<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"

For this week\u2019s Technology Feature, Michael Eisenstein wrote about the technology, applications, and challenges of nanopore DNA sequencing. In brief, the technology involves threading intact pieces of DNA through a\u00a0tiny aperture in a membrane or other barrier,\u00a0through which a current flows. As each base passes,\u00a0it disrupts that current in a characteristic way, allowing the sequence to be determined.  Read more<\/a> Continue reading →<\/span><\/a><\/p>\n","protected":false},"author":104777,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[192,200],"tags":[72611,5945961,8703483,8703487,8703485,6677357,75],"class_list":["post-15315","post","type-post","status-publish","format-standard","hentry","category-blog-2","category-technology-2","tag-bioinformatics","tag-jeffrey-perkel","tag-nanopore-sequencing","tag-nicholas-loman","tag-oxford-nanopore-technologies","tag-techblog","tag-technology"],"_links":{"self":[{"href":"https:\/\/blogs.nature.com\/naturejobs\/wp-json\/wp\/v2\/posts\/15315","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blogs.nature.com\/naturejobs\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blogs.nature.com\/naturejobs\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.nature.com\/naturejobs\/wp-json\/wp\/v2\/users\/104777"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.nature.com\/naturejobs\/wp-json\/wp\/v2\/comments?post=15315"}],"version-history":[{"count":0,"href":"https:\/\/blogs.nature.com\/naturejobs\/wp-json\/wp\/v2\/posts\/15315\/revisions"}],"wp:attachment":[{"href":"https:\/\/blogs.nature.com\/naturejobs\/wp-json\/wp\/v2\/media?parent=15315"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.nature.com\/naturejobs\/wp-json\/wp\/v2\/categories?post=15315"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.nature.com\/naturejobs\/wp-json\/wp\/v2\/tags?post=15315"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}