BOL: Related items

BBMap help

Shruti Paniwala — Mon, 10 Oct 2016 06:29:03 -0500

BBMAP • a solution for everything

That content has been reformatted and it is being expanded to include more information.

There are common options for most BBMap suite programs and depending on the file extension the input/output format is automatically chosen/set.

Using BBMap

Mapping Nanopore reads

BBMap.sh has a length cap of 6kbp. Reads longer than this will be broken into 6kbp pieces and mapped independently.

More at https://www.biostarhandbook.com/tools/bbmap/bbmap-help.html

Address of the bookmark: https://www.biostarhandbook.com/tools/bbmap/bbmap-help.html

Beagle

Jit — Thu, 27 Oct 2016 11:19:00 -0500

Beagle is a software package that performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection.

Beagle version 4.1 has a more accurate genotype phasing algorithm and a very fast and accurate genotype imputation algorithm. Version 4.1 also has several changes to the command line arguments which are described in the release notes. The "ped" argument has no effect in version 4.1. If your data contains nuclear families and you want to model the parent-offspring relationships when phasing genotypes, please use version 4.0.

If you use Beagle 4.1 in a published analysis, please report the program version and cite the appropriate article.

The citation for Beagle's phasing algorithm is:

S R Browning and B L Browning (2007) Rapid and accurate haplotype phasing and missing data inference for whole genome association studies by use of localized haplotype clustering. Am J Hum Genet 81:1084-1097.doi:10.1086/521987

The citation for Beagle's genotype imputation algorithm is:

B L Browning and S R Browning (2016). Genotype imputation with millions of reference samples. Am J Hum Genet 98:116-126.doi:10.1016/j.ajhg.2015.11.020

The citation for Beagle's IBD detection algorithm is:

B L Browning and S R Browning (2013). Improving the accuracy and efficiency of identity-by-descent detection in population data. Genetics 194(2):459-71.doi:10.1534/genetics.113.150029

Address of the bookmark: http://faculty.washington.edu/browning/beagle/beagle.html

Statistics Using R with Biological Examples

Neel — Thu, 03 Nov 2016 04:55:41 -0500

This book is a manifestation of my desire to teach researchers in biology a bit more about statistics than an ordinary introductory course covers and to introduce the utilization of R as a tool for analyzing their data. My goal is to reach those with little or no training in higher level statistics so that they can do more of their own data analysis, communicate more with statisticians, and appreciate the great potential statistics has to offer as a tool to answer biological questions.

This is necessary in light of the increasing use of higher level statistics in biomedical research. I hope it accomplishes this mission and encourage its free distribution and use as a course text or supplement.

K Seefeld, May 2007

MyPro: A seamless pipeline for automated prokaryotic genome assembly and annotation

Neel — Thu, 15 Dec 2016 05:47:35 -0600

MyPro is an improved genomics software pipeline for prokaryotic genomes. MyPro is user-friendly and requires minimal programming skills. High-quality prokaryotic genome assembly and annotation can be obtained with ease. It performed better than de novo assemblers and contig integration software. Produces more contiguous assemblies, higher N50 values and lower number of contigs.

More at https://sourceforge.net/projects/sb2nhri/files/MyPro/

Address of the bookmark: http://www.sciencedirect.com/science/article/pii/S0167701215001207

coursera genome assembly tutorial

Jit — Sat, 25 Nov 2017 08:57:25 -0600

Solutions to Coursera Genome Sequencing (Bioinformatics II)

Address of the bookmark: https://github.com/iansealy/coursera-assembly

COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly

Jit — Wed, 06 Dec 2017 02:08:14 -0600

An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE connected over 99% of reads with 98.8% accuracy, which is, respectively, 10 and 2% higher than the recently published tool FLASH. When COPE is applied to real reads for genome assembly, the resulting contigs are found to have fewer errors and give a 14-fold improvement in the N50 measurement when compared with the contigs produced using unconnected reads.

Address of the bookmark: ftp://ftp.genomics.org.cn/pub/cope

Cgaln

Jit — Wed, 22 Feb 2017 05:14:15 -0600

Cgaln (Coarse grained alignment) is a program designed to align a pair of whole genomic sequences of not only bacteria but also entire chromosomes of vertebrates on a nominal desktop computer. Cgaln performs an alignment job in two steps, at the block level and then at the nucleotide level. The former "coarse-grained" alignment can explore genomic rearrangements and reduce the regions to be analyzed in the next step. The latter is devoted to detailed alignment within the limited regions found in the first stage. The output of Cgaln is 'glocal' in the sense that rearrangements are taken into consideration while each alignable region is extended as long as possible. Thus, Cgaln is not only fast and memory-efficient, but also can filter noisy outputs without missing the most important homologous segment pairs.

http://www.iam.u-tokyo.ac.jp/chromosomeinformatics/rnakato/cgaln/

Address of the bookmark: http://www.iam.u-tokyo.ac.jp/chromosomeinformatics/rnakato/cgaln/

DIAL

Abhimanyu Singh — Wed, 01 Mar 2017 08:42:28 -0600

A computational pipeline for identifying single-base substitutions between two closely related genomes without the help of a reference genome. DIAL works even when the depth of coverage is insufficient for de novo assembly, and it can be extended to determine small insertions/deletions. Our main motivation is to use this tool to survey the genetic diversity of endangered species as the identified sequence differences can be used to design genotyping arrays to assist in the species' management.

http://www.bx.psu.edu/~ratan/

Address of the bookmark: http://www.bx.psu.edu/miller_lab/

QUAST-LG: Versatile genome assembly evaluation

Jit — Thu, 25 Oct 2018 10:46:55 -0500

QUAST-LG-a tool that compares large genomic de novo assemblies against reference sequences and computes relevant quality metrics. Since genomes generally cannot be reconstructed completely due to complex repeat patterns and low coverage regions, we introduce a concept of upper bound assembly for a given genome and set of reads, and compute theoretical limits on assembly correctness and completeness. Using QUAST-LG, we show how close the assemblies are to the theoretical optimum, and how far this optimum is from the finished reference.

AVAILABILITY AND IMPLEMENTATION:

http://cab.spbu.ru/software/quast-lg

Address of the bookmark: http://cab.spbu.ru/software/quast-lg/

Krona

Jit — Wed, 22 Mar 2017 04:47:35 -0500

Krona allows hierarchical data to be explored with zooming, multi-layered pie charts. Krona charts can be created using an Excel template or KronaTools, which includes support for several bioinformatics tools and raw data formats. The interactive charts are self-contained and can be viewed with any modern web browser (see Browser support).

Address of the bookmark: https://github.com/marbl/Krona/wiki