User:Jarle Pahr/Assembly

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0075505

Useful links

http://www.homolog.us/blogs/blog/2013/01/10/two-helpful-guides-for-those-working-on-genome-assembly/

http://www.homolog.us/blogs/blog/2013/06/07/de-novo-nssembly-is-not-at-all-black-art/

http://trinity.engr.uconn.edu/~vamsik/Fragment%20Assembly/NagarajanPopJCB09.pdf

https://courseware.stanford.edu/pg/assignments/view/317058/assignment-1-string-fragment-reassembly

Genome assembly review papers: http://www.biostars.org/p/52178/

Write a genome assembler with BLASR and Python: http://nbviewer.ipython.org/urls/raw.github.com/cschin/Write_A_Genome_Assembler_With_IPython/master/Write_An_Assembler.ipynb

http://www.homolog.us/blogs/blog/2013/05/07/genome-assembly-programs-what-hash-functions-do-they-use/

CUBELP genome assembly tutorial: http://elvis.ccc.cranfield.ac.uk/CUBELP2/faces/Genome.xhtml

Software

http://nbviewer.ipython.org/url/files.figshare.com/1009027/Write_An_Assembler.ipynb

SOAP DeNovo

http://soap.genomics.org.cn/soapdenovo.html

Minimus

http://sourceforge.net/apps/mediawiki/amos/index.php?title=Minimus2

HGAP

HGAP: https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/HGAP

Velvet

Velvet:

http://www.molecularevolution.org/resources/activities/velvet_and_bowtie_activity

AbySS

Abyss: http://www.bcgsc.ca/platform/bioinfo/software/abyss

Newbler

Newbler: http://seqanswers.com/wiki/Newbler

Minia

http://minia.genouest.org/

Minia: http://www.homolog.us/blogs/blog/2012/10/01/minia-assembly-algorithm-and-french-revolution/

MINIA on Raspberry Pi – assembling a 100 Mbp genome on a credit card sized computer: http://f1000.com/posters/browse/summary/1093759

http://minia.genouest.org/ : "Minia is a short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day."

Using cascading Bloom filters to improve the memory usage for de Brujin graphs: http://arxiv.org/abs/1302.7278

Contig assembly using Minia: http://evomics.org/learning/assembly-and-alignment/minia/

MIRA

MIRA: http://sourceforge.net/apps/mediawiki/mira-assembler/index.php?title=Main_Page

Cortex

Cortex

http://bioinformatics.oxfordjournals.org/content/early/2012/11/19/bioinformatics.bts673.full.pdf+html

http://cortexassembler.sourceforge.net/

http://www.homolog.us/blogs/blog/2012/12/12/exploring-single-sample-snp-and-indel-calling-with-whole-genome-assembly/

http://www.homolog.us/blogs/blog/2013/01/11/high-throughput-microbial-population-genomics-using-the-cortex-variation-assembler/

https://twitter.com/richardmleggett/status/211944292128796672/photo/1/large

A5 assembly pipeline

A5 assembly pipeline:

http://code.google.com/p/ngopt/wiki/A5PipelineREADME

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0042304

http://www.youtube.com/watch?v=ePGUIj9Qbvc

Presentations

http://www.slideshare.net/c.titus.brown/2013-stampsintroassembly-25057638?utm_source=slideshow&utm_medium=ssemail&utm_campaign=upload_digest

http://ged.msu.edu/angus/tutorials-2013/files/rayan-2013-june-18-msu.pdf

Quality control

QUAST: http://bioinf.spbau.ru/quast

http://www.homolog.us/blogs/blog/2013/05/02/assessment-of-assembly/

Hawkeye: http://www.ncbi.nlm.nih.gov/pubmed/17349036

De novo likelihood-based measures for comparing genome assemblies: http://www.biomedcentral.com/content/pdf/1756-0500-6-334.pdf

Bibliography

http://genome.cshlp.org/content/early/2009/12/16/gr.097261.109.full.pdf+html

GAGE-B: An Evaluation of Genome Assemblers for Bacterial Organisms: http://bioinformatics.oxfordjournals.org/content/early/2013/05/10/bioinformatics.btt273.short

http://www.ncbi.nlm.nih.gov/pubmed/20211242