# install.packages('VennDiagram')
library(VennDiagram)

Second step: Load data

Add filepath if “catdoge.csv” is not in working-directory.

d <- read.csv("catdoge.csv")

Address of the bookmark: http://rstudio-pubs-static.s3.amazonaws.com/13301_6641d73cfac741a59c0a851feb99e98b.html

Note that the information on this page is targeted at end-users. For developers, the source code, building instructions and implementation/development resources are available on GitHub.

The Picard toolkit is open-source under the MIT license and free for all uses.

Enjoy!

Address of the bookmark: http://broadinstitute.github.io/picard/

into contiguous sequences (called contigs). One can use the sequences of different sequencing technologies either in a single assembly run (a true hybrid assembly) or by mapping one type of data to an assembly of other sequencing type (a semi-hybrid assembly (or mapping)) or by mapping a data against consensus sequences of other assemblies (a simple mapping).

The MIRA acronym stands for Mimicking Intelligent Read Assembly and the program pretty well does what its acronym says (well, most of the time anyway). It is the Swiss army knife of sequence assembly that I've used and developed during the past 14 years to get assembly jobs I work on done efficiently - and especially accurately. That is, without me actually putting too much manual work into it.

More at http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html

Address of the bookmark: http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html

Manual at http://spades.bioinf.spbau.ru/release3.7.1/manual.html

Address of the bookmark: http://bioinf.spbau.ru/spades

More at https://gatb.inria.fr/

Address of the bookmark: https://gatb.inria.fr/

More at http://www.vicbioinformatics.com/software.vague.shtml

Address of the bookmark: http://www.vicbioinformatics.com/software.vague.shtml

Training Resources:

• Bioinformatics Workshop (Webinars)
• Bioinformatics Training Slides

Specialized Applications:

• De Novo Assembly
• Transcriptome analysis
• Base Modification Analysis
• Barcoding
• Data Analysis Tools
• Minor Variants and Phasing Analysis

Address of the bookmark: https://github.com/PacificBiosciences/Bioinformatics-Training/wiki

Download

Minia 2.0.7 Linux 64-bits binaries (Source code) (Legacy codebase)

For the impatient

A typical Minia command line looks like:

./minia -in reads.fa -kmer-size 31 -abundance-min 3 -out output_prefix

Type

./minia

for a quick explanation of the parameters.

For more information, refer to the manual.

KmerGenie can be used to determine the best k-mer size, minimum abundance of correct k-mers, and genome size estimation for your dataset.

Address of the bookmark: http://minia.genouest.org/

Cutadapt helps with these trimming tasks by finding the adapter or primer sequences in an error-tolerant way. It can also modify and filter reads in various ways. Adapter sequences can contain IUPAC wildcard characters. Also, paired-end reads and even colorspace data is supported. If you want, you can also just demultiplex your input data, without removing adapter sequences at all.

Cutadapt comes with an extensive suite of automated tests and is available under the terms of the MIT license.

If you use cutadapt, please cite DOI:10.14806/ej.17.1.200 .

More at https://github.com/marcelm/cutadapt

Address of the bookmark: http://cutadapt.readthedocs.io/en/stable/guide.html

Address of the bookmark: http://garm-meta-assem.sourceforge.net/