BOL: Related items

Picard

Neel — Fri, 29 Apr 2016 08:21:54 -0500

Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file formats are defined in the Hts-specs repository. See especially the SAM specification and the VCF specification.

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/

Sequence assembly with MIRA 4

Priya Singh — Wed, 06 Apr 2016 08:21:22 -0500

MIRA is a multi-pass DNA sequence data assembler/mapper for whole genome and EST/RNASeq projects. MIRA assembles/maps reads gained by

electrophoresis sequencing (aka Sanger sequencing)
454 pyro-sequencing (GS20, FLX or Titanium)
Ion Torrent
Solexa (Illumina) sequencing
(in development) Pacific Biosciences sequencing

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

Understanding Fastqc Output

Jit — Fri, 15 Apr 2016 05:47:40 -0500

Understanding Following table and graphs

Duplication level
kmer profile
per base GC content
per base N content
per base quality
per base sequence content
per sequence GC content
per sequence quality
sequence length distribution

More at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/

Address of the bookmark: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/

ALE: a Generic Assembly Likelihood Evaluation Framework for Assessing the Accuracy of Genome and Metagenome Assemblies

Neel — Tue, 26 Apr 2016 03:38:43 -0500

Assembly Likelihood Evaluation (ALE) framework that overcomes these limitations, systematically evaluating the accuracy of an assembly in a reference-independent manner using rigorous statistical methods. This framework is comprehensive, and integrates read quality, mate pair orientation and insert length (for paired-end reads), sequencing coverage, read alignment and k-mer frequency. ALE pinpoints synthetic errors in both single and metagenomic assemblies, including single-base errors, insertions/deletions, genome rearrangements and chimeric assemblies presented in metagenomes. At the genome level with real-world data, ALE identifies three large misassemblies from the Spirochaeta smaragdinae finished genome, which were all independently validated by Pacific Biosciences sequencing. At the single-base level with Illumina data, ALE recovers 215 of 222 (97%) single nucleotide variants in a training set from a GC-rich Rhodobacter sphaeroides genome. Using real Pacific Biosciences data, ALE identifies 12 of 12 synthetic errors in a Lambda Phage genome, surpassing even Pacific Biosciences' own variant caller, EviCons. In summary, the ALE framework provides a comprehensive, reference-independent and statistically rigorous measure of single genome and metagenome assembly accuracy, which can be used to identify misassemblies or to optimize the assembly process.

More at http://www.ncbi.nlm.nih.gov/pubmed/23303509

Address of the bookmark: http://sc932.github.io/ALE/about.html

Bambus

Jit — Tue, 16 Aug 2016 08:09:15 -0500

Bambus 2.0, the second generation Bambus scaffolder available as an open source package. While most other scaffolders are closely tied to a specific assembly program, Bambus accepts the output from most current assemblers and provides the user with great flexibility in choosing the scaffolding parameters. In particular, Bambus is able to accept contig linking data other than specified by mate-pairs. Such sources of information include alignment to a reference genome (Bambus can directly use the output of MUMmer), physical mapping data, or information about gene synteny.

Home Page:

http://sourceforge.net/apps/mediawiki/amos/index.php?title=Bambus2

Address of the bookmark: https://www.cbcb.umd.edu/software/bambus2

NGS teaching material

Jit — Wed, 05 Apr 2017 04:29:06 -0500

High throughput sequencing (HTS) technologies are being applied to a wide range of important topics in biology. However, the analyses of non-model organisms, for which little previous sequence information is available, pose specific problems. This course addresses the specific strengths and weaknesses of alternative HTS technologies, the computational resources needed for HTS, and how to analyze non-model species using HTS. The course consists of a practical training module, HTS bioinformatics training, and lecturing/seminars of HTS approaches specifically targeting non-model organisms.

Address of the bookmark: http://marinetics.org/teaching/hts/Assembly.html

Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm

BioStar — Mon, 16 Mar 2020 10:09:26 -0500

Apollo is an assembly polishing algorithm that attempts to correct the errors in an assembly. It can take multiple set of reads in a single run and polish the assemblies of genomes of any size. Described by Firtina et al. (preliminary version at https://arxiv.org/pdf/1902.04341.pdf

More at https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa179/5804978?rss=1

Address of the bookmark: https://github.com/CMU-SAFARI/Apollo

A simple tutorial for a complex ComplexHeatmap

Neel — Fri, 02 Apr 2021 06:18:32 -0500

ComplexHeatmap (Gu, Eils, and Schlesner (2016)) is an R Programming Language (R Core Team (2020)) package that is currently listed in the Bioconductor package repository.

install and load required packages

  require(RColorBrewer)
  require(ComplexHeatmap)
  require(circlize)
  require(digest)
  require(cluster)

If all load successfully, proceed to Part 3. Otherwise, go through the following code chunks in order to ensure that each package is installed and loaded properly.

BiocManager (Morgan (2019))

Address of the bookmark: https://github.com/kevinblighe/E-MTAB-6141

HNADOCK: a nucleic acid docking server for modeling RNA/DNA–RNA/DNA 3D complex structures

Poonam Mahapatra — Thu, 04 Jun 2020 23:19:07 -0500

The HNADOCK server is to predict the binding complex structure between two nucleic acid molecules through a hierarchical docking algorihtm of an FFT-based global search strategy and an intrinsic scoring function for nucleic acid interactions. Users are required to provide the three-dimensional (3D) structures of the two molecules to be docked.

Address of the bookmark: http://huanglab.phys.hust.edu.cn/hnadock/

IQ-TREE: Efficient software for phylogenomic inference

Jit — Mon, 18 Feb 2019 04:25:11 -0600

A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time

IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3–97.1%. IQ-TREE is freely available at http://www.cibiv.at/software/iqtree

Address of the bookmark: http://www.iqtree.org/