C Chiang, R M Layer, G G Faust, M R Lindberg, D B Rose, E P Garrison, G T Marth, A R Quinlan, and I M Hall. SpeedSeq: ultra-fast personal genome analysis and interpretation. Nat Meth (2015). doi:10.1038/nmeth.3505.

http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3505.html

Address of the bookmark: https://github.com/hall-lab/speedseq

Know of any other open source software for PacBio data? Email us.

Software categories:

• De novo assembly
• Structural Variations Detection
• Reference-based alignment
• Consensus and variant calling
• RNA analysis
• Epigenetic base modifications and methylation
• Barcoding
• Genome Browsers
• Run QC
• Frameworks and APIs

Address of the bookmark: https://github.com/PacificBiosciences/DevNet/wiki/Compatible-Software

QuorUM is distributed as an independent software package and as a module of the MaSuRCA assembly software. Both are available under the GPL open source license at http://www.genome.umd.edu.

Address of the bookmark: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0130821

HECIL’s core algorithm by introducing an iterative learning paradigm that enhances the correction policy at each iteration by incorporating knowledge gathered from previous iterations via data-driven confidence metrics assigned to prior corrections.

Address of the bookmark: https://github.com/NDBL/HECIL

Address of the bookmark: http://pacb.com/blog/the-hifi-difference-true-long-reads-vs-synthetic-long-reads/

Before you go down that path, consider this critical biological question:
Are you sequencing human cells—or bacterial contamination?

The Silent Saboteur: Mycoplasma in Cell Cultures

Mycoplasma contamination remains one of the most widespread and underdiagnosed issues in tissue culture work. Studies suggest that 15–35% of cell lines in use may be contaminated, often without visible signs. Unlike other microbial infections, Mycoplasma does not produce cloudiness, odor, or a change in pH. Many researchers won’t detect it unless they specifically test for it.

The consequences, however, are profound. Mycoplasma can significantly alter:

• Host gene expression patterns

• Cell proliferation rates

• Epigenetic profiles and chromatin accessibility

• Cytokine signaling and immune responses

In short, it can skew your results, compromise your biological conclusions, and invalidate weeks or months of research.

A Simple Diagnostic Step: Map Against Mycoplasma Genomes

If you encounter poor alignment rates to the human genome, consider mapping your reads to a Mycoplasma reference genome—or better yet, use a combined human + Mycoplasma reference. There have been cases where over half of all reads, initially assumed to be from human cells, were in fact bacterial in origin. This check is fast, easy, and could save your project.

How Contamination Happens—and Persists

Mycoplasma is small (0.1–0.3 μm), lacks a cell wall, and can pass through standard filters undetected. Common sources include:

• Contaminated reagents (e.g., FBS)

• Infected cell lines obtained from other labs

• Poor aseptic technique or shared equipment

Once present, it spreads quickly between cultures and can persist for months, silently affecting results.

Why Treatment Is Difficult

While antibiotics such as Plasmocin or BM-Cyclin are sometimes used, they often offer only partial resolution and may themselves alter cell behavior. In many cases, the best course of action is to discard the contaminated culture and start with a fresh, verified stock.

Practical Recommendations for Researchers

• Routinely test for Mycoplasma using PCR, qPCR, or fluorescence-based assays

• Incorporate contamination screens into your sequencing QC pipeline

• Use combined reference genomes when mapping ambiguous reads

• Practice strict aseptic technique and monitor all incoming cell lines

• Don’t ignore unexplained data anomalies—they might point to contamination

Closing Thought: Contamination Is a Biological Variable

It’s easy to view poor mapping as a technical issue, but sometimes the problem lies deeper—in the biology itself. Mycoplasma contamination doesn’t just interfere with sequencing; it interferes with science. As a research community, we must treat contamination not as an afterthought, but as a key variable to control.

So next time your reads won’t align, don’t just tune the aligner. Ask if your cells are telling the truth—or if they're hiding something.

Source: Life technologies

Address of the bookmark: http://www.lifetechnologies.com/global/en/home/communities-social/blog/blogs/sequencing-solutions-to-world-health.html?cid=social_blogseries_20130829_11098264

Title: Comparison of Short Read De Novo Alignment Algorithms 

Author: Nikhil Gopal

Address of the bookmark: http://biochem218.stanford.edu/Projects%202011/Gopal%202011.pdf

http://bmi.osu.edu/hpc/software/benchmark/

http://bmi.osu.edu/hpc/software/pmap/pmap.html

Other similiar papers:

http://online.liebertpub.com/doi/pdf/10.1089/cmb.2012.0022

http://bioinformatics.oxfordjournals.org/content/28/24/3169

Some new Mapping tool links:

GSNAP

http://research-pub.gene.com/gmap/

RMAP

http://rulai.cshl.edu/rmap/

mrsFAST

http://mrsfast.sourceforge.net/Home

http://sourceforge.net/projects/mrsfast/files/mrsfast-ultra-3.1.0/

BFAST

http://sourceforge.net/apps/mediawiki/bfast/index.php?title=Main_Page

SHRiMP (for AB SOLiD color-space reads)

http://compbio.cs.toronto.edu/shrimp/

RazerA 3

http://www.seqan.de/projects/razers/

Address of the bookmark: http://www.biomedcentral.com/1471-2105/14/184

Related Paper:

http://genomebiology.com/2014/15/3/R59/abstract

Address of the bookmark: http://www.news.ucdavis.edu/search/news_detail.lasso?id=10859