BOL: Related items

International Conference on Bioinformatics Models, Methods and Algorithms

Rahul Agarwal — Sun, 05 Oct 2014 11:42:52 -0500

The purpose of the International Conference on Bioinformatics Models, Methods and Algorithms is to bring together researchers and practitioners interested in the application of computational systems and information technologies to the field of molecular biology, including for example the use of statistics and algorithms to understanding biological processes and systems, with a focus on new developments in genome bioinformatics and computational biology. Areas of interest for this community include sequence analysis, biostatistics, image analysis, scientific data management and data mining, machine learning, pattern recognition, computational evolutionary biology, computational genomics and other related fields.

Position Paper Submission Extension: October 9, 2014
Regular Paper Authors Notification: November 3, 2014
Position Paper Authors Notification: November 6, 2014
Regular and Position Paper Camera Ready and Registration: November 17, 2014

Address of the bookmark: http://www.bioinformatics.biostec.org/

1mb long DNA with Nanopore technology

Jit — Tue, 19 Dec 2017 18:49:28 -0600

The first continuous DNA read of more than a million bases (>1Mb) has been achieved, using Oxford Nanopore sequencing technology. Congratulations to Martin Smith and collaborators! Read more: http://bit.ly/2j5TNCO

Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data

Jit — Thu, 19 Apr 2018 08:06:03 -0500

Heap, that enables robustly sensitive and accurate calling of SNPs, particularly with a low coverage NGS data, which must be aligned to the reference genome sequences in advance. To reduce false positive SNPs, Heap determines genotypes and calls SNPs at each site except for sites at the both end of reads or containing a minor allele supported by only one read. Performance comparison with existing tools showed that Heap achieved the highest F-scores with low coverage (7X) restriction-site associated DNA sequencing reads of sorghum and rice individuals. This will facilitate cost-effective GWAS and GP studies in this NGS era. Code and documentation of Heap are freely available from https://github.com/meiji-bioinf/heap and our web site (http://bioinf.mind.meiji.ac.jp/lab/en/tools.html).

Address of the bookmark: https://github.com/meiji-bioinf/heap

HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies

Jit — Tue, 15 May 2018 07:35:26 -0500

HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just work" with excellent speed and accuracy. We found that previously described haplotype assembly methods are specialized for specific read technologies or protocols, with slow or inaccurate performance on others. With this in mind, HapCUT2 is designed for speed and accuracy across diverse sequencing technologies, including but not limited to: NGS short reads (Illumina HiSeq) clone-based sequencing (Fosmid or BAC clones) SMRT reads (PacBio) Oxford Nanopore reads 10X Genomics Linked-Reads proximity-ligation (Hi-C) reads high-coverage sequencing (>40x coverage-per-SNP) using above technologies combinations of the above technologies (e.g. scaffold long reads with Hi-C reads) See below for specific examples of command line options and best practices for some of these technologies. NOTE: At this time HapCUT2 is for diploid organisms only. VCF input should contain diploid variants. If you use HapCUT2 in your research, please cite: Edge, P., Bafna, V. & Bansal, V. HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies. Genome Res. gr.213462.116 (2016). doi:10.1101/gr.213462.116

Address of the bookmark: https://github.com/vibansal/HapCUT2

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

SimLoRD: A read simulator for third generation sequencing reads

Aaryan Lokwani — Wed, 22 Aug 2018 10:40:27 -0500

SimLoRD is a read simulator for third generation sequencing reads and is currently focused on the Pacific Biosciences SMRT error model.

Reads are simulated from both strands of a provided or randomly generated reference sequence.

The reference can be read from a FASTA file or randomly generated with a given GC content. It can consist of several chromosomes, whose structure is respected when drawing reads. (Simulation of genome rearrangements may be incorporated at a later stage.)
The read lengths can be determined in four ways: drawing from a log-normal distribution (typical for genomic DNA), sampling from an existing FASTQ file (typical for RNA), sampling from a a text file with integers (RNA), or using a fixed length
Quality values and number of passes depend on fragment length.
Provided subread error probabilities are modified according to number of passes
Outputs reads in FASTQ format and alignments in SAM format

Address of the bookmark: https://bitbucket.org/genomeinformatics/simlord/

Qualimap2: Evaluating next generation sequencing alignment data

Jit — Tue, 11 Sep 2018 04:44:29 -0500

Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.

Supported types of experiments include:

Whole-genome sequencing
Whole-exome sequencing
RNA-seq (speical mode available)
ChIP-seq

Address of the bookmark: http://qualimap.bioinfo.cipf.es/

sim3C: Read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC)

Jit — Tue, 13 Nov 2018 07:25:38 -0600

Required python modules

biopython
intervaltree
numpy
scipy
tqdm
PyYAML

Address of the bookmark: https://github.com/cerebis/sim3C

NGS Platforms launched by BGI’s MGI Tech

Jit — Thu, 10 Jan 2019 04:42:06 -0600

MGI Tech Co., Ltd. (MGI), a subsidiary of BGI Group, is committed to enabling effective and affordable healthcare solutions for all. Based on its proprietary technology, MGI produces sequencing devices, equipment, consumables and reagents to support life science research, medicine and healthcare. MGI's multi-omics platforms include genetic sequencing, mass spectrometry and medical imaging. Providing real-time, comprehensive, life-long solutions, its mission is to develop and promote advanced life science tools for future healthcare.

MGI, a subsidiary of global genomics leader BGI Group, announced pricing and its first early access customer for the new ultra high-throughput sequencer, MGISEQ-T7, saying it has driven down sequencing cost to $5 per gigabyte, with exceptionally high accuracy. Such innovations are helping more people to realize the benefits of genomic information.

In October, MGI launched the MGISEQ-T7, a highly flexible production-scale platform that is the most powerful sequencer to date. It can produce as many as 60 whole human genomes in one day. The instrument sells for $1 million.

The T7 enables simultaneous but independent operation of up to four flow cells, which means different applications such as single-cell RNA sequencing, whole exome sequencing and whole genome sequencing can be run in different flow cells at the same time. This helps to reduce costs, allowing MGI to offer the most competitive sequencing price in the market.

Powered by DNBseq™, MGISEQ delivers quality data with accuracy for SNP and Indel calling rate of 99.9% and 99%, respectively, along with decreased duplication rate down to less than 2 percent, and almost zero Index mis-assignment rate.

SOURCE MGI

https://www.bgi.com/global/company/news/bgis-mgi-tech-launches-two-new-ngs-platforms/

http://en.mgitech.cn/

jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator

Abhimanyu Singh — Fri, 26 Jul 2019 00:58:12 -0500

jackalope simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina and Pacific Biosciences (PacBio) platforms. It can either read reference genomes from FASTA files or simulate new ones. Genomic variants can be simulated using summary statistics, phylogenies, Variant Call Format (VCF) files, and coalescent simulations—the latter of which can include selection, recombination, and demographic fluctuations. jackalope can simulate single, paired-end, or mate-pair Illumina reads, as well as reads from Pacific Biosciences These simulations include sequencing errors, mapping qualities, multiplexing, and optical/PCR duplicates. All outputs can be written to standard file formats.

A swift, versatile phylogenomic and high-throughput sequencing simulator https://jackalope.lucasnell.com

Address of the bookmark: https://github.com/lucasnell/jackalope