BOL: Related items

AIRVF: a filtering toolbox for precise variant calling in Ion Torrent sequencing

BioStar — Fri, 22 Dec 2017 00:31:06 -0600

AIRVF that works on flowgram, raw and mapped reads and called variants to reduce artifact-driven false variant calls. Tests on sequencing data of standard reference material showed up to ∼98% reduction of false variants when combined to conventional public pipelines and ∼48% to the in-house commercial solution, with a minimal loss of sensitivity

The program with a detailed manual is available at https://sourceforge.net/projects/airvf/

Address of the bookmark: https://sourceforge.net/projects/airvf/

ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.

Seema Singh — Mon, 30 Apr 2018 04:38:40 -0500

ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set.

Detail paper at https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3927-8

Address of the bookmark: https://github.com/VicugnaPacos/ALPACA

Circlator: automated circularization of genome assemblies using long sequencing reads

Poonam Mahapatra — Tue, 15 May 2018 09:42:32 -0500

A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Circlator: automated circularization of genome assemblies using long sequencing reads", Hunt et al, Genome Biology 2015 Dec 29;16(1):294. doi: 10.1186/s13059-015-0849-0. PMID: 26714481.

Address of the bookmark: http://sanger-pathogens.github.io/circlator/

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

NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data

Jit — Mon, 06 Aug 2018 17:24:53 -0500

NextSV, a meta SV caller and a computational pipeline to perform SV calling from low coverage long-read sequencing data. NextSV integrates three aligners and three SV callers and generates two integrated call sets (sensitive/stringent) for different analysis purpose. The output of NextSV is in ANNOVAR-compatible bed format. Users can easily perform downstream annotation using ANNOVAR and disease gene discovery using Phenolyzer.

Address of the bookmark: https://github.com/Nextomics/NextSV

Indexcov: fast coverage quality control for whole-genome sequencing

Jit — Wed, 29 Aug 2018 09:20:46 -0500

indexcov, an efficient estimator of whole-genome sequencing coverage to rapidly identify samples with aberrant coverage profiles, reveal large-scale chromosomal anomalies, recognize potential batch effects, and infer the sex of a sample. Indexcov is available at https://github.com/brentp/goleft under the MIT license.

Address of the bookmark: https://github.com/brentp/goleft

d2Tools: The toolbox for counting the frequency of k-tuple from sequencing datasets and calculate the dissimilarity

Jit — Thu, 20 Sep 2018 08:38:29 -0500

d2Tools are the toolbox for counting the frequency of K-tuple from sequencing datasets and then calculating the pairwise dissimilarity matrix between samples with the d2-style(d2/d2*/d2S representing d2/d2Star/d2shepp, respectively) measures. Hao, Dai, Eucliean, Mahattan, and Chebyshev distance measures are also included in d2Tools.

Manual at https://code.google.com/archive/p/d2-tools/wikis/d2ToolMannual.wiki

Address of the bookmark: https://code.google.com/archive/p/d2-tools/

lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data

BioJoker — Tue, 27 Nov 2018 04:43:57 -0600

lordFAST is a sensitive tool for mapping long reads with high error rates. lordFAST is specially designed for aligning reads from PacBio sequencing technology but provides the user the ability to change alignment parameters depending on the reads and application.

lordFAST, a novel long-read mapper that is specifically designed to align reads generated by PacBio and potentially other SMS technologies to a reference. lordFAST not only has higher sensitivity than the available alternatives, it is also among the fastest and has a very low memory footprint.

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

Katuali is a flexible consensus pipeline implemented in Snakemake to basecall, assemble, and polish Oxford Nanopore Technologies' sequencing data

Jit — Tue, 22 Jan 2019 06:26:55 -0600

Run a pipeline processing fast5s to a consensus in a single command.
Recommended fixed "standard" and "fast" pipelines.
Interchange basecaller, assembler, and consensus components of the pipelines simply by changing the target filepath.
Seemless distribution of tasks over local or distributed compute.
Highly configurable.
Open source (Mozilla Public License 2.0).

Documentation can be found at https://nanoporetech.github.io/katuali/.

Address of the bookmark: https://github.com/nanoporetech/katuali

Prof. Dr. med. Andreas Ramming

Wed, 07 Aug 2019 03:25:48 -0500

In many autoimmune diseases, a misdirected immune response leads to chronic inflammation and subsequently to fibrotic and degenerative tissue remodeling. Therapeutic options are available for inflammatory joint diseases, but only about 40% of patients respond to these existing therapies on a permanent basis. In the remaining cases, these therapies miss their target from the beginning or later during the course of treatment failure. There are currently no causal therapies available for the treatment of fibrotic autoimmune diseases such as systemic sclerosis. Therefore, there is an urgent need to develop new therapeutic options for the treatment of fibrotic and synovitic autoimmune diseases. His group is therefore deal with the molecular mechanisms of these misdirected signaling pathways for the development of novel, targeted therapies

http://www.medizin3.uk-erlangen.de/forschung/arbeitsgruppen/matrixbiologie-entzuendliche-signalwege-in-arthritis-und-fibrose/