BOL: Related items

CHSMiner: a GUI tool to identify chromosomal homologous segments

Jit — Sat, 18 Nov 2017 16:55:49 -0600

Background

The identification of chromosomal homologous segments (CHS) within and between genomes is essential for comparative genomics. Various processes including insertion/deletion and inversion could cause the degeneration of CHSs.

Results

Here we present a Java software CHSMiner that detects CHSs based on shared gene content alone. It implements fast greedy search algorithm and rigorous statistical validation, and its friendly graphical interface allows interactive visualization of the results. We tested the software on both simulated and biological realistic data and compared its performance with similar existing software and data source.

Conclusion

CHSMiner is characterized by its integrated workflow, fast speed and convenient usage. It will be useful for both experimentalists and bioinformaticians interested in the structure and evolution of genomes.

https://github.com/zhenwang100/CHSMiner

Address of the bookmark: https://almob.biomedcentral.com/articles/10.1186/1748-7188-4-2

jobTree based python wrapper to run the genome simulation tool suite Evolver

Jit — Fri, 08 Dec 2017 16:26:32 -0600

evolverSimControl (eSC) can be used to simulate multi-chromosome genome evolution on an arbitrary phylogeny (Newick format). In addition to simply running evolver, eSC also automatically creates statistical summaries of the simulation as it runs including text and image files. Also included are convenience scripts to: check on a running simulation and see detailed status and logging information; extract fasta sequence files from the leaf nodes of a completed simulation; extract pairwise multiple alignment files (.maf) from leaf and branch nodes from a completed simulation and with the help of mafJoin, join them together into a single maf covering the entire simulation.

Address of the bookmark: https://github.com/dentearl/evolverSimControl

CAMSA :: a tool for Comparative Analysis and Merging of Scaffold Assemblies

Rahul Nayak — Thu, 28 Dec 2017 09:10:26 -0600

CAMSA – is a tool for Comparative Analysis and Merging of Scaffold Assemblies, distributed both as a standalone software package and as Python library under the MIT license.

Main features:

works with any number of scaffold assemblies in de-novo non-progressive fashion
allows to simultaneously work with scaffold assemblies obtained from any in silico and in vitro techniques, supporting multiple existing formats via built-in converters
creates an extensive report with several comparative quality metrics (both on assembly level and on the level of individual assembly points)
constructs a merged combined scaffold assembly
provides an interactive framework for a visual comparative analysis of the given assemblies

Address of the bookmark: https://cblab.org/camsa/

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

“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files

Poonam Mahapatra — Mon, 04 Jun 2018 03:45:15 -0500

One code to find them all is a set of perl scripts to extract useful information from RepeatMasker about transposable elements, retrieve their sequences and get some quantitative information. Assemble RepeatMasker hits into complete TE copies, including LTR-retrotransposon Retrieve corresponding TE sequences, and flanking sequences, from the local fasta files Compute summary statistics for each TE family (number of TE copies, genome coverage...) Ambiguous cases such as nested TE can be assembled into copies automatically or manually Allow for working with a TE user-defined library Allow for working with only a user-chosen set of TE families http://doua.prabi.fr/software/one-code-to-find-them-all

Address of the bookmark: http://doua.prabi.fr/software/one-code-to-find-them-all

SALSA: A tool to scaffold long read assemblies with Hi-C

Jit — Fri, 15 Jun 2018 04:01:15 -0500

This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch. To use the latest version, first run the following commands: cd SALSA make To run the code, you will need Python 2.7, BOOST libraries and Networkx(version lower than 1.2). If you consider using this tool, please cite our publication which describes the methods used for scaffolding. Ghurye, J., Pop, M., Koren, S., Bickhart, D., & Chin, C. S. (2017). Scaffolding of long read assemblies using long range contact information. BMC genomics, 18(1), 527. Link Ghurye, J., Rhie, A., Walenz, B.P., Schmitt, A., Selvaraj, S., Pop, M., Phillippy, A.M. and Koren, S., 2018. Integrating Hi-C links with assembly graphs for chromosome-scale assembly. bioRxiv, p.261149 Link For any queries, please either ask on github issue page or send an email to Jay Ghurye (jayg@cs.umd.edu).

Address of the bookmark: https://github.com/machinegun/SALSA

gSearch: a fast and flexible general search tool for whole-genome sequencing

Jit — Mon, 06 Aug 2018 17:19:15 -0500

gSearch compares sequence variants in the Genome Variation Format (GVF) or Variant Call Format (VCF) with a pre-compiled annotation or with variants in other genomes. Its search algorithms are subsequently optimized and implemented in a multi-threaded manner.

Address of the bookmark: http://ml.ssu.ac.kr/gSearch/index.html

LRCstats: a tool for evaluating long reads correction methods

Aaryan Lokwani — Wed, 22 Aug 2018 11:05:04 -0500

LRCstats is an open-source pipeline for benchmarking DNA long read correction algorithms for long reads outputted by third generation sequencing technology such as machines produced by Pacific Biosciences. The reads produced by third generation sequencing technology, as the name suggests, are longer in length than reads produced by next generation sequencing technologies, such as those produced by Illumina. However, long reads are plagued by high error rates, which can cause issues in downstream analysis. Long read correction algorithms reduce the error rate of long reads either through self-correcting methods or using accurate, short reads outputted by next generation sequencing technologies to correct long reads.

Address of the bookmark: https://github.com/cchauve/lrcstats

GRSR: a tool for deriving genome rearrangement scenarios from multiple unichromosomal genome sequences

Jit — Fri, 28 Sep 2018 09:35:10 -0500

GRSR is a Tool for Deriving Genome Rearrangement Scenarios for Multiple Uni-chromosomal Genomes. This tool will do the following steps:

Step 1. Run mugsy to get multiple sequence alignment results.
Step 2 & 3. Extraction of the Coordinates of Core Blocks, Construction of Synteny Blocks and Generating Signed Permutations.
Step 4. Generate pairwise genome rearrangement scenarios and find repeats at the breakpoints of each rearrangement events.

https://github.com/DanwangJessica/GRSR

Address of the bookmark: https://github.com/DanwangJessica/GRSR

SENIOR RESEARCH FELLOW at All India Institute of Medical Sciences (AIIMS Delhi) - Delhi, Delhi

Wed, 11 Mar 2015 03:06:10 -0500

Applications are invited from eligible candidates for the following temporary post in an ICMR funded Research Project entitle “An Investigation to find out reasons for Phenotypic Heterogeneity/Variability in 22q11.2 Microdeletion Syndrome” in Department of Reproductive Biology, AIIMS, New Delhi PI: Dr. Ashutosh Halder, Professor, Department of Reproductive Biology

Name of the post: Senior Research Fellow (SRF)
Duration: 2 year
Salary: Rs. 28000/- per month + 30% HRA
Eligibility: MSc (life sciences) with 2 years research experience, NET/GATE qualified
Desirable: Experience in the field of Genomics, Epigenomics & Bioinformatics
SELECTION PROCEDURE FOR ALL INDIA INSTITUTE OF MEDICAL SCIENCES (AIIMS DELHI) – SENIOR RESEARCH FELLOW POST:

Candidates can apply on or before 15/03/2015
No Detailed information about the selection process is mentioned in the recruitment notification
HOW TO APPLY FOR SENIOR RESEARCH FELLOW VACANCY IN ALL INDIA INSTITUTE OF MEDICAL SCIENCES (AIIMS DELHI):

Deadline: 15.03.15 Submit your C.V in Room No. 2099 (Molecular Cytogenetics Lab), 2nd floor, Reproductive Biology, All India Institute of Medical Sciences, New Delhi-110029 or Email CV to: ashutoshhalder@gmail.com Your CV should include the details of your work experience & degrees along with two references with e-mail and contact number Only 10 shortlisted (on merit) candidates will be invited for interview. No TA/DA will be applicable for the same