BOL: Related items

CSBB-v1.0

Neel — Wed, 29 Jun 2016 07:33:05 -0500

CSBB is a command line based bioinformatics suite to analyze biological data acquired through varied avenues of biological experiments. CSBB is implemented in Perl, while it also leverages the use of R and python in background for specific modules. Major focus of CSBB is to allow users from biology and bioinformatics community, to get benefited by performing down-stream analysis tasks while eliminating the need to write programming code. CSBB is currently available on Linux, UNIX, MAC OS and Windows platforms.

Currently CSBB provides 13 modules focused on analytical tasks like performing upper-quantile normalization on expression data or convert genome wide gene expression to z-scores when comparing expression data from different platforms.

More at https://github.com/skygenomics/CSBB-v1.0

Address of the bookmark: https://github.com/skygenomics/CSBB-v1.0

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

valet

Jit — Thu, 22 Sep 2016 04:27:09 -0500

VALET is a pipeline for performing de novo validation of metagenomic assemblies. VALET checks a number of properties that should hold true for a correct assembly (e.g., mate-pairs are aligned at the correct distance from each other in the assembly, the depth of coverage is fairly uniform along contigs, etc.). The violations of these invariants are reported allowing one to pinpoint areas that were potentially mis-assembled, or to compare the quality of different assemblies. For comparing multiple assemblies of the same data-sets, VALET also reports an overall estimate of the likelihood a particular assembly is correct.

Home Page:

VALET code repository

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

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

RepeatModeler

Jit — Thu, 18 Aug 2016 09:57:15 -0500

RepeatModeler is a de-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats.

Address of the bookmark: http://www.repeatmasker.org/RepeatModeler.html

SRF Bioinformatics job position in National Institute of Plant Genome Research (NIPGR)

Mon, 19 Sep 2016 05:43:38 -0500

SRF Bioinformatics job position in National Institute of Plant Genome Research (NIPGR)
Title : “Transcriptome and small RNA diversity analysis of developing seed contrasting rice varieties”
Qualification : Candidates having M.Sc./M.Tech. degree or equivalent (with minimum 60% marks) in Bioinformatics with a minimum of two years of post M.Sc./M.Tech research experience are eligible to apply.
No. of Post : 01
How to apply
Application should reach to Dr. Pinky Agarwal, Staff Scientist, National Institute of Plant Genome Research (NIPGR) Aruna Asaf Ali Marg, P.O. Box NO. 10531, New Delhi - 110067 on or before 30/09/2016

More at http://www.nipgr.res.in/careers/vacancies_latest.php#

LUMPY

Shruti Paniwala — Thu, 25 Aug 2016 08:05:02 -0500

A probabilistic framework for structural variant discovery.

Ryan M Layer, Colby Chiang, Aaron R Quinlan, and Ira M Hall. 2014. "LUMPY: a Probabilistic Framework for Structural Variant Discovery." Genome Biology 15 (6): R84. doi:10.1186/gb-2014-15-6-r84.

More at https://github.com/arq5x/lumpy-sv

Address of the bookmark: https://github.com/arq5x/lumpy-sv

Ka, Ks and Ka/Ks calculations

Poonam Mahapatra — Mon, 29 Aug 2016 11:44:11 -0500

gKaKs is a codon-based genome-level Ka/Ks computation pipeline developed and based on programs from four widely used packages: BLAT, BLASTALL (including bl2seq, formatdb and fastacmd), PAML (including codeml and yn00) and KaKs_Calculator (including 10 substitution rate estimation methods). gKaKs can automatically detect and eliminate frameshift mutations and premature stop codons to compute the substitution rates (Ka, Ks and Ka/Ks) between a well-annotated genome and a non-annotated genome or even a poorly assembled scaffold dataset. It is especially useful for newly sequenced genomes that have not been well annotated.

Look for KaKs calculation:

https://github.com/fumba/kaks-calculator

http://longlab.uchicago.edu/?q=gKaKs

http://www.ncbi.nlm.nih.gov/pubmed/23314322

Address of the bookmark: http://longlab.uchicago.edu/?q=gKaKs

BRAKER: pipeline for fully automated prediction of protein coding genes with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes

Jit — Thu, 01 Sep 2016 08:02:59 -0500

Gene finding in eukaryotic genomes is notoriously difficult to automate. The task is to design a work flow with a minimal set of tools that would reach state-of-the-art performance across a wide range of species. GeneMark-ET is a gene prediction tool that incorporates RNA-Seq data into unsupervised training and subsequently generates ab initio gene predictions. AUGUSTUS is a gene finder that usually requires supervised training and uses information from RNA-Seq reads in the prediction step. Complementary strengths of GeneMark-ET and AUGUSTUS provided motivation for designing a new combined tool for automatic gene prediction.

http://www.ncbi.nlm.nih.gov/pubmed/26559507

Address of the bookmark: http://bioinf.uni-greifswald.de/bioinf/braker/

Nanopolis: polish a genome assembly

Rahul Nayak — Thu, 26 Jul 2018 04:51:28 -0500

Software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more (see Nanopolish modules, below).

Quickstart

http://nanopolish.readthedocs.io/en/latest/quickstart_consensus.html

Algorithms

http://simpsonlab.github.io/2017/06/30/nanopolish-v0.7.0/

Address of the bookmark: https://github.com/jts/nanopolish