BOL: Related items

HASLR: a tool for rapid genome assembly of long sequencing reads

LEGE — Fri, 31 Jan 2020 05:50:15 -0600

HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation Sequencing reads (such as Illumina) from the same sample.

Address of the bookmark: https://github.com/vpc-ccg/haslr

Parliament2: Runs a combination of tools to generate structural variant calls on whole-genome sequencing data

Jit — Thu, 28 May 2020 21:57:03 -0500

Parliament2 identifies structural variants in a given sample relative to a reference genome. These structural variants cover large deletion events that are called as Deletions of a region, Insertions of a sequence into a region, Duplications of a region, Inversions of a region, or Translocations between two regions in the genome.

Parliament2 runs a combination of tools to generate structural variant calls on whole-genome sequencing data. It can run the following callers: Breakdancer, Breakseq2, CNVnator, Delly2, Manta, and Lumpy. Because of synergies in how the programs use computational resources, these are all run in parallel. Parliament2 will produce the outputs of each of the tools for subsequent investigation.

Address of the bookmark: https://github.com/dnanexus/parliament2

Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data

Neel — Fri, 25 Feb 2022 04:42:09 -0600

This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovB / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc.

Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example:

Address of the bookmark: https://github.com/KamilSJaron/smudgeplot

LASTZ

Abhi — Mon, 18 Apr 2016 04:41:55 -0500

LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454.

More at http://www.bx.psu.edu/~rsharris/lastz/

Thesis: http://www.bx.psu.edu/~rsharris/rsharris_phd_thesis_2007.pdf

Address of the bookmark: http://www.bx.psu.edu/~rsharris/lastz/

Postdoctoral Fellowship in Bioinformatics at pesolelab

Thu, 01 Oct 2015 07:20:48 -0500

Job Description: Bioinformatics postdoc positions are available in the area of genomics with main focus on exome and RNAseq technologies by ultra high-throughput sequencing platforms. Successful applicants should have the following qualities:

1) demonstrated experience in Bioinformatics research,
2) programing experience (python and/or R, C and C++ are very welcome),
3) knowledge of Linux/Unix environment,
4) experience in handling deep-seq data,
5) highly motivated and hard working, and
6) interested to work with a multi-disciplinary team combining bioinformatics, genomics, computational biology approaches with experimental biology.

Our research interest covers different areas of bioinformatics and genomics in order to achieve a deeper understanding of gene and genome structure and function (please look at our PubMed publications for more details about our research http://www.ncbi.nlm.nih.gov/pubmed/?term=pesole+g).

Interested applicants should email the curriculum vitae to Prof. Graziano Pesole at graziano.pesole@uniba.it or Dr. Ernesto Picardi at Ernesto.picardi@uniba.it.

Start date: immediate

Duration: up to 24 months
Contact Person (Referent): Ernesto Picardi
Ref. E-Mail: ernesto.picardi@uniba.it
Tel: +390805443308
Fax: +390805443317

Group Web Page: http://www.pesolelab.it/

Project Fellow Positions at CSIR-IHBT Palampur

Tue, 01 Dec 2015 05:45:58 -0600

Walk-in-Interview is scheduled to be held on the date as mentioned below for selection of Suitable candidates in the following areas under the different Sponsored/CSIR Networked Projects on purely temporary basis for the duration of the project(s) or till completion of projects whichever is earlier:

Sponsored/CSIR Networked Project:
(i) Genomics and Informatics Solutions for Integrating Biology (GENESIS)" [BSC-0121] (up to March, 2017).
(ii) Profiling and characterization of early phase differential mi-RNA (s) responsible for downstream developmen of insulin resistance in hMSC derived adipocytes. (GAP-0188) [up to 31.03.2018].

Position: Project Fellow (2 position)
Age : 28 years as on 18.12.15
Salary : Rs.12,000/- P.M.
Rs.14,000/- P.M.
as per the funds provisions in the respective projects.
Eligibility Criteria : 1st Class B. Tech. in Bioinformatics/ Computational Biology
OR
M.Sc. in Bioinformatics/ Computational Biology with 55% marks
OR
M.Tech. in Bioinformatics/ Computational Biology with 55% marks
OR
M.Sc. in any field of Life Science with Diploma in Bioinformatics

Selection Procedure : Walk In Interview

Date : 18 Dec , 2015
Time : 10:00 A.M.
Venue : CSIR-IHBT Palampur (H.P.)