BOL: Related items

Java utilities for Next Generation Sequencing by Pierre Lindenbaum

Robert M Willioms — Mon, 15 Sep 2014 17:24:49 -0500

Java utilities for Bioinformatics

Address of the bookmark: https://github.com/lindenb/jvarkit

Shasta long read assembler

Jit — Tue, 14 Jan 2020 06:47:07 -0600

The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells.

Computational methods used by the Shasta assembler include:

Using a run-length representation of the read sequence. This makes the assembly process more resilient to errors in homopolymer repeat counts, which are the most common type of errors in Oxford Nanopore reads.
Using in some phases of the computation a representation of the read sequence based on markers, a fixed subset of short k-mers (k ≈ 10).

More at https://chanzuckerberg.github.io/shasta/index.html

Address of the bookmark: https://github.com/chanzuckerberg/shasta

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

KAD: Assessing genome assemblies using K-mer copies in assemblies and K-mer abundance in Illumina reads

Jit — Fri, 19 Jun 2020 07:34:12 -0500

KAD is designed for evaluating the accuracy of nucleotide base quality of genome assemblies. Briefly, abundance of k-mers are quantified for both sequencing reads and assembly sequences. Comparison of the two values results in a single value per k-mer, K-mer Abundance Difference (KAD), which indicates how well the assembly matches read data for each k-mer.

where, c is the count of a k-mer from reads, m is the mode of counts of read k-mers, and n is the copy of the k-mer in the assembly.

Address of the bookmark: https://github.com/liu3zhenlab/KAD

JRF in Bioinformatics @ Bioinformatics Centre, North-Eastern Hill University

Thu, 06 Nov 2014 10:24:05 -0600

Applications with complete bio-data are invited for JRF (3) and Project Assistant (1) in a DBT project "Next Generation Sequencing (NGS)-based de novo assembly of expressed transcripts and genome information of Orchids in North-East India" sanctioned for a period of 3 years.

Details are available at www.nehu.ac.in and www.bicnehu.ac.in.

Applications must reach the undersigned within 15 days from the date of publication of this advertisement.

Prof. Pramod Tandon. PI/Mr. Devendra Kumar Biswal (Co-PI)

GenomeTools: The versatile open source genome analysis software

Neel — Wed, 02 Feb 2022 04:00:21 -0600

The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named “libgenometools” which consists of several modules.

If you are interested in gene prediction, have a look at GenomeThreader.

http://genometools.org/pub/

Address of the bookmark: http://genometools.org/

dcGOR

Martin Jones — Sat, 08 Nov 2014 14:54:28 -0600

An R package for analysing ontologies and protein domain annotations has been published in PLoS Computational Biology (http://dx.doi.org/10.1371/journal.pcbi.1003929). The package is distributed as part of CRAN (http://cran.r-project.org/package=dcGOR), and also at GitHub for version control.

The dedicated website is available in http://supfam.org/dcGOR, from which several demos are also provided:

1. Analysing SCOP domains: http://supfam.org/dcGOR/demo-Fang.html

2. Analysing Pfam domains: http://supfam.org/dcGOR/demo-Basu.html

3. Analysing InterPro domains: http://supfam.org/dcGOR/demo-Customisation.html

Refseq viraal genome sequences !

Jit — Sat, 11 Dec 2021 08:35:18 -0600

List of all viruses on NCBI

https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/

Address of the bookmark: https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/

ICGEB Bioinformatics RA/SRF/JRF Vacancies

Thu, 13 Nov 2014 13:39:30 -0600

Research Associate/JRF/SRF position, DBT Sponsored Bioinformatics Infrastructure Facility

Applicants should hold a PhD or a first class MSc/MTech degree in Bioinformatics of Biotechnology/Life Sciences; experience in using bioinformatics tools, working in Linux and knowledge of computer network administration.

Submit CV and letter of interest by email to: Dr. Dinesh Gupta atdinesh@icgeb.res.in

CrossMap: program for genome coordinates conversion between different assemblies

Rahul Nayak — Tue, 25 Jan 2022 17:59:32 -0600

CrossMap is a program for genome coordinates conversion between different assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used file formats including BAM, CRAM, SAM, Wiggle, BigWig, BED, GFF, GTF, MAF VCF, and gVCF.

Address of the bookmark: http://crossmap.sourceforge.net/