BOL: Related items

Termal: a fast and interactive terminal-based viewer for multiple sequence alignments

LEGE — Mon, 22 Sep 2025 23:51:02 -0500

termal, a fast, interactive, terminal-based viewer for multiple sequence alignments (MSAs), designed for use on remote systems such as high-performance computing (HPC) clusters.

https://academic.oup.com/bioinformaticsadvances/advance-article/doi/10.1093/bioadv/vbaf208/8257678?login=true

Address of the bookmark: https://github.com/sib-swiss/termal

SVEngine: Allele Specific and Haplotype Aware Structural Variants Simulator

Jit — Sat, 04 Jul 2020 05:52:34 -0500

SVEngine (Structural Variants Engine)

SVEngine is a multi-purpose and self-contained simulator for whole genome scale spike-in of thousands of SV events of various types in both single-sample and matched sample scenarios.
SVEngine takes as input reference contigs in FASTA files, variant meta distribution as specified in META files (see Manual) or specific variant information as specified in VAR files (see Manual) and NEWICK files for specifying clonal phylogenetic trees in cancer.
SVEngine outpus alterred contigs in FASTA files, spiked-in variants in VAR files (see Manual), simulated short read in FASTQ files and aligned short reads in BAM files.

Address of the bookmark: https://bitbucket.org/charade/svengine/src/master/

Fellowship (Doctoral Research In Biomedical Genomics, Including Statistical Genomics)

Sun, 20 Dec 2015 06:03:43 -0600

Fellowship (Doctoral Research In Biomedical Genomics, Including Statistical Genomics)
Eligibility : MSc(Bio-Chemistry, Bio-Informatics, Bio-Tech, Mathematics / Applied Mathematics, Stati, Zoology)
Location : Kolkata
Last Date : 31 Dec 2015
Hiring Process : Written-test

NO: 340/ESTB/ADMN/NIBMG/2015-16
Doctoral Research In Biomedical Genomics, Including Statistical Genomics conduct National Institute of Biomedical Genomics (NIBMG)
Information For Students Interested To Pursue Doctoral Research In Biomedical Genomics, Including Statistical Genomics, At The National Institute Of Biomedical Genomics (Nibmg), Kalyan
Eligibility conditions for specific areas of research are :
Statistical Genomics : An applicant who wishes to pursue research in Statistical Genomics should hold a Master's degree (First class or equivalent) in a relevant discipline (Statistics, Mathematics, Bioinformatics, or a related discipline)
Biomedical Genomics : An applicant who wishes to pursue research in any area of biomedical genomics, other than statistical genomics, should hold a Master's degree (First class or equivalent) in a relevant discipline (Biochemistry, Biotechnology, Molecular Biology, Genetics, Zoology, Physiology, or a related discipline)
Fellowship : An applicant should have passed the NET conducted by CSIR/UGC/ICMR/DBT within the past ONE year AND should have been awarded a valid Junior Research Fellowship from CSIR, UGC, ICMR, DBT (Category-I only), DST (INSPIRE), NBHM. Preference will be given to candidates with demonstrable research training in the form of summer training or short-term courses in established research laboratories in preparation for a research career in biomedical sciences
How to apply
Online application will be accepted until 5 PM of December 31, 2015. A formal interview of the short-listed candidates will be held on January 12, 2016

More at http://www.nibmg.ac.in/?q=Career%20Opportunities

nQuire: a statistical framework for ploidy estimation using next generation sequencing

Jit — Thu, 04 Oct 2018 05:23:59 -0500

nQuire provides a statistical framework to study organisms with intraspecific variation in ploidy. nQuire is likely to be useful in epidemiological studies of pathogens, artificial selection experiments, and for historical or ancient samples where intact nuclei are not preserved. It is implemented as a stand-alone Linux command line tool in the C programming language and is available at https://github.com/clwgg/nQuireunder the MIT license.

Address of the bookmark: https://github.com/clwgg/nQuireunder

SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis

BioStar — Mon, 17 Aug 2020 05:21:09 -0500

SHAMAN is a shiny application for differential analysis of metagenomic data (16S, 18S, 23S, 28S, ITS and WGS) including bioinformatics treatment of raw reads for targeted metagenomics, statistical analysis and results visualization with a large variety of plots (barplot, boxplot, heatmap, …).
The bioinformatics treatment is based on Vsearch [Rognes 2016] which showed to be both accurate and fast [Wescott 2015].The statistical analysis is based on DESeq2 R package [Anders and Huber 2010] which robustly identifies the differential abundant features as suggested in [McMurdie and Holmes 2014] and [Jonsson2016]. SHAMAN robustly identifies the differential abundant genera with the Generalized Linear Model implemented in DESeq2 [Love 2014].
SHAMAN is compatible with standard formats for metagenomic analysis (.csv, .tsv, .biom) and figures can be downloaded in several formats. A presentation about SHAMAN is available here and a poster here.

More at https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03666-4

Address of the bookmark: https://github.com/aghozlane/shaman

TAREAN: A computational tool for identification and characterization of satellite DNA from unassembled short reads

Surabhi Chaudhary — Tue, 15 May 2018 02:53:11 -0500

TAndem REpeat ANalyzer -TAREAN – is a computational pipeline for unsupervised identification of satellite repeats from unassembled sequence reads. The pipeline uses low-pass whole genome sequence reads and performs their graph-based clustering. Resulting clusters, representing all types of repeats, are then examined for the presence of circular structures and putative satellite repeats are reported.

How to use TAREAN:

Install a local instance of the pipeline using its source code available from bitbucket repository.
Use public Galaxy-based server at https://repeatexplorer-elixir.cerit-sc.cz/. The server is provided in frame of the Elixir CZ project and is maintained by CESNET and CERIT-SC. Simple registration is required to use this service.

Development of TAREAN was supported by ELIXIR CZ research infrastructure project (MEYS Grant No: LM2015047).

References

Novak, P., Avila Robledillo, L., Koblizkova, A., Vrbova, I., Neumann, P., Macas, J. (2017) – TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads. Nucleic Acids Res., doi:10.1093/nar/gkx257

Address of the bookmark: https://bitbucket.org/petrnovak/repex_tarean

Scaffolding of a bacterial genome using MinION nanopore sequencing

Rahul Agarwal — Tue, 07 Jul 2015 16:59:25 -0500

Second generation sequencing has revolutionized genomic studies. However, most genomes contain repeated DNA elements that are longer than the read lengths achievable with typical sequencers, so the genomic order of several generated contigs cannot be easily resolved. A new generation of sequencers offering substantially longer reads is emerging, notably the Pacific Biosciences (PacBio) RS II system and the MinION system, released in early 2014 by Oxford Nanopore Technologies through an early access program.

Address of the bookmark: http://www.nature.com/srep/2015/150707/srep11996/full/srep11996.html

Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome

Jit — Wed, 29 Nov 2017 05:08:53 -0600

Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become available that we used for sequencing the S. cerevisiae genome. To make use of these data, we developed a novel open-source hybrid error correction algorithm Nanocorr (https://github.com/jgurtowski/nanocorr) specifically for Oxford Nanopore reads, as existing packages were incapable of assembling the long read lengths (5-50kbp) at such high error rate (between ~5 and 40% error). With this new method we were able to perform a hybrid error correction of the nanopore reads using complementary MiSeq data and produce a de novo assembly that is highly contiguous and accurate: the contig N50 length is more than ten-times greater than an Illumina-only assembly (678kb versus 59.9kbp), and has greater than 99.88% consensus identity when compared to the reference. Furthermore, the assembly with the long nanopore reads presents a much more complete representation of the features of the genome and correctly assembles gene cassettes, rRNAs, transposable elements, and other genomic features that were almost entirely absent in the Illumina-only assembly.

Address of the bookmark: http://schatzlab.cshl.edu/data/nanocorr/

The MARVEL assembler

Jit — Fri, 04 May 2018 19:18:41 -0500

MARVEL consists of a set of tools that facilitate the overlapping, patching, correction and assembly of noisy (not so noisy ones as well) long reads.

The assembly process can be summarized as follows:

overlap
patch reads
overlap (again)
scrubbing
assembly graph construction and touring
optional read correction
fasta file creation

Address of the bookmark: https://github.com/schloi/MARVEL

npScarf: real-time scaffolder using SPAdes contigs and Nanopore sequencing reads

Shruti Paniwala — Mon, 11 Jun 2018 05:14:57 -0500

npScarf (jsa.np.npscarf) is a program that connect contigs from a draft genomes to generate sequences that are closer to finish. These pipelines can run on a single laptop for microbial datasets. In real-time mode, it can be integrated with simple structural analyses such as gene ordering, plasmid forming.

Address of the bookmark: http://japsa.readthedocs.io/en/latest/tools/jsa.np.npscarf.html