BOL: Related items

Pacasus: Correction of palindromes in long reads from PacBio and Nanopore

BioStar — Mon, 12 Nov 2018 05:26:48 -0600

Tool for detecting and cleaning PacBio / Nanopore long reads after whole genome amplification. Check the poster from the Revolutionizing Next-Generation Sequencing (2nd edition) conference in the source folder: https://github.com/swarris/Pacasus/blob/master/vib2017.pdf.

The prepint version is found on http://www.biorxiv.org/content/early/2017/08/09/173872

It uses the pyPaSWAS framework for sequence alignment (https://github.com/swarris/pyPaSWAS)

Address of the bookmark: https://github.com/swarris/Pacasus

LoRMA: A tool for correcting sequencing errors in long reads

Abhimanyu Singh — Thu, 06 Sep 2018 16:21:01 -0500

An error correction method that uses long reads only. The method consists of two phases: first, we use an iterative alignment-free correction method based on de Bruijn graphs with increasing length of k-mers, and second, the corrected reads are further polished using long-distance dependencies that are found using multiple alignments. According to our experiments, the proposed method is the most accurate one relying on long reads only for read sets with high coverage. Furthermore, when the coverage of the read set is at least 75×, the throughput of the new method is at least 20% higher.

conda install -c atgc-montpellier lorma

Address of the bookmark: https://gite.lirmm.fr/lorma/lorma-releases/wikis/home

Bandage: interactive visualization of de novo genome assemblies

Shruti Paniwala — Mon, 04 Dec 2017 10:09:37 -0600

Bandage (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily) is a tool for visualizing assembly graphs with connections. Users can zoom in to specific areas of the graph and interact with it by moving nodes, adding labels, changing colors and extracting sequences. BLAST searches can be performed within the Bandage graphical user interface and the hits are displayed as highlights in the graph. By displaying connections between contigs, Bandage presents new possibilities for analyzing de novo assemblies that are not possible through investigation of contigs alone.

Availability and implementation: Source code and binaries are freely available at https://github.com/rrwick/Bandage. Bandage is implemented in C++ and supported on Linux, OS X and Windows. A full feature list and screenshots are available at http://rrwick.github.io/Bandage.

Address of the bookmark: http://rrwick.github.io/Bandage/

MITOS: improved de novo metazoan mitochondrial genome annotation

Jit — Fri, 26 Oct 2018 08:25:39 -0500

Allows automatic annotation of metazoan mitochondrial genomes. MITOS is a pipeline designed to compute a consistent de novo annotation of the mitogenomic sequences. The software allows for a systematic error screening, the standardisation of gene name and gene boundary designation, anticodon labelling of tRNAs, and provides the means for the assessment of the validity of a gene assignment.

Address of the bookmark: http://mitos.bioinf.uni-leipzig.de/index.py

Integrative Meta-Assembly Pipeline (IMAP): Chromosome-level genome assembler combining multiple de novo assemblies

Jit — Sat, 31 Aug 2019 11:30:41 -0500

Chromosome-level genome assembler combining multiple de novo assemblies

https://github.com/jkimlab/IMAP

Address of the bookmark: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0221858

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/

New born babies get ready to know their whole genome soon!!!

Rahul Agarwal — Thu, 05 Sep 2013 07:24:02 -0500

USA launch a pilot projects to examine medical information of newborn baby, which are being funded by the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) and the National Human Genome Research Institute (NHGRI), both parts of the National Institutes of Health.

Awards of $5 million to four grantees have been made in fiscal year 2013 under the Genomic Sequencing and Newborn Screening Disorders research program. The program will be funded at $25 million over five years, as funds are made available.

"Hundreds of US babies will be pioneers in genomic medicine through a US$25-million programme to sequence their genomes soon after they are born."

Source:

http://blogs.nature.com/news/2013/09/scientists-to-sequence-hundreds-of-newborns-genomes.html

http://www.genome.gov/27554919

GOLD:Genomes Online Database

Jit — Wed, 26 Jul 2017 07:49:29 -0500

GOLD:Genomes Online Database, is a World Wide Web resource for comprehensive access to information regarding genome and metagenome sequencing projects, and their associated metadata, around the world.

https://gold.jgi.doe.gov/

Address of the bookmark: https://gold.jgi.doe.gov/

Magic-BLAST: a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome.

Jit — Tue, 26 Dec 2017 22:23:39 -0600

Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of RNA-seq, locating the candidate introns and adding up the score of all exons. This is very different from other versions of BLAST, where each exon is scored as a separate hit and read-pairing is ignored.

Magic-BLAST incorporates within the NCBI BLAST code framework ideas developed in the NCBI Magic pipeline, in particular hit extensions by local walk and jump (http://www.ncbi.nlm.nih.gov/pubmed/26109056), and recursive clipping of mismatches near the edges of the reads, which avoids accumulating artefactual mismatches near splice sites and is needed to distinguish short indels from substitutions near the edges.

Address of the bookmark: https://ncbi.github.io/magicblast/

JBrowse: Embeddable genome browser built completely with JavaScript and HTML5

Jit — Fri, 29 Jun 2018 09:19:56 -0500

JBrowse is a fast, embeddable genome browser built completely with JavaScript and HTML5, with optional run-once data formatting tools written in Perl. Headline Features: Fast, smooth scrolling and zooming. Explore your genome with unparalleled speed. Scales easily to multi-gigabase genomes and deep-coverage sequencing. Quickly open and view data files on your computer without uploading them to any server. Supports GFF3, BED, FASTA, Wiggle, BigWig, BAM, VCF (with either .tbi or .idx index), REST, and more. BAM, BigBed, BigWig, and VCF data are displayed directly from chunks of the compressed binary files, no conversion needed. Includes an optional “faceted” track selector (see demo) suitable for large installations with thousands of tracks. Very light server resource requirements. In fact, JBrowse has no back-end server code, just tools for formatting data files to be read directly over HTTP. Serve huge datasets from a single low-cost cloud instance. Can run as a stand-alone app on OSX and Windows using the Electron platform Highly extensible plugin architecture, with a large plugin registry of existing examples here https://gmod.github.io/jbrowse-registry https://jbrowse.org/

Address of the bookmark: https://github.com/GMOD/jbrowse