BOL: Related items

Integrative Genomics Viewer (IGV) tutorial

Neel — Sat, 12 Jul 2014 15:16:23 -0500

The Integrative Genomics Viewer (IGV) from the Broad Center allows you to view several types of data files involved in any NGS analysis that employs a reference genome, including how reads from a dataset are mapped, gene annotations, and predicted genetic variants.

http://www.broadinstitute.org/igv/

Address of the bookmark: https://wikis.utexas.edu/display/bioiteam/Integrative+Genomics+Viewer+%28IGV%29+tutorial

COSMOS, our workflow management system for NGS data

Jit — Wed, 23 Jul 2014 07:29:14 -0500

COSMOS, our Python-based management system for implementing large-scale parallel workflows focusing on, but not restricted to, large-scale short-read "NGS" sequencing data is open-access published via Advance Access in Bioinformatics (Gafni et al. 2014). It is also available for download for non-commercial academic and research purposes at:

http://cosmos.hms.harvard.edu/.

Address of the bookmark: https://cosmos.hms.harvard.edu/

Swabs to Genomes: A Comprehensive Workflow

Rahul Nayak — Sun, 10 Aug 2014 03:01:21 -0500

The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become almost trivial for research labs with access to standard molecular biology and computational tools. However, there are a wide variety of options available for DNA library preparation and sequencing, and inexperience with bioinformatics can pose a significant barrier to entry for many who may be interested in microbial genomics. The objective of the present study was to design, test, troubleshoot, and publish a simple, comprehensive workflow from the collection of an environmental sample (a swab) to a published microbial genome; empowering even a lab or classroom with limited resources and bioinformatics experience to perform it.

Address of the bookmark: https://peerj.com/preprints/453.pdf

fragScaff: Genome Assembly with Contiguity Preserving Transposition

Jit — Mon, 14 May 2018 04:28:14 -0500

Contiguity preserving transposition and sequencing (CPT-seq) is an entirely in vitro means of generating libraries comprised of 9216 indexed pools, each of which contains thousands of sparsely sequenced long fragments ranging from 5 kilobases to >1 megabase. This software, fragScaff, leverages coincidences between the content of different pools as a source of contiguity information for scaffolding de novo genome assemblies. FragScaff is complementary to Lachesis, providing midrange contiguity to support robust, accurate chromosome-scale de novo genome assemblies without the need for laborious in vivo cloning steps.

Further information about fragScaff, including source code, is available at:https://sourceforge.net/projects/fragscaff/files.

Manuscript describing fragScaff was published as: Adey A, Kitzman JO, Burton JN, Daza R, Kumar A, Christiansen L, Ronaghi M, Amini S, L Gunderson K, Steemers FJ, Shendure J#. In vitro, long-range sequence information for de novo genome assembly via transposase contiguity. Genome Research 2014 Dec;24(12):2041-9. doi: 10.1101/gr.178319.114. PubMed PMID: 25327137.

Address of the bookmark: https://sourceforge.net/projects/fragscaff/files/

You can't hide from Genome Hackers

Neel — Sat, 13 Oct 2018 14:17:28 -0500

Young computational biologist named Yaniv Erlich shocked the research world by showing it was possible to unmask the identities of people listed in anonymous genetic databases using only an Internet connection

Paper: http://science.sciencemag.org/content/early/2018/10/10/science.aau4832

More at https://www.wired.com/story/genome-hackers-show-no-ones-dna-is-anonymous-anymore/

Software developed in pevsner lab

Robert M Willioms — Mon, 06 Oct 2014 12:41:26 -0500

DRAGON: Database Referencing of Array Genes Online

SNOMAD: Standardization and Normalization of Microarray Data

SNPduo: SNP Analysis Between Two Individuals

SNPtrio: Analyzing and Visualizing and Inheritance Patterns in Trios

SNPscan: Data Analysis and Visualization of SNP Data

pediSNP: Analyze SNP Data From a Pedigree of Two Generations

kcoeff: Calculate Cotterman Coefficients of SNP Genotype Data

triPOD: Detects chromosomal abnormalities in parent-child trio-based microarray data

Address of the bookmark: http://pevsnerlab.kennedykrieger.org/php/?q=software

Libraries or management tools for high throughput sequencing data

LEGE — Fri, 04 Oct 2024 02:45:06 -0500

GATB Library. The Genome Analysis Toolbox with de-Bruijn graph. A large part of tools developed by the GenScale team are based on this library.
These methods enable the analysis of data sets of any size on multi-core desktop computers, including very huge amount of reads data coming from any kind of organisms such as bacteria, plants, animals and even complex samples (e.g. metagenomes). Among them are (the full is available here: https://gatb.inria.fr/software/):
LRez: C++ Library and toolkit for the barcode-based management and indexation of linked-read datasets.

Variant calling and/or genotyping

DiscoSNP++ and discoSnpRAD: Reference-free small variant discovery (SNPs and indels)
MindTheGap: Detection and assembly of large insertion variants
TakeABreak: reference-free inversion discovery tool
SVJedi: Structural Variant genotyper with long read data
SVJedi-graph: Structural Variant genotyper with long read data using a variation graph

Sequence assembly

MinYS: reference-guided genome assembly in metagenomics data
MTG-link: local assembly tool for linked-read data
Minia: De novo short read assembler
de-novo pipeline: de-novo assembly pipeline (error correction / contigs / scaffolding) for genomes and meta-genomes
Mapsembler2: Targeted assembly (not maintained)

Managing k-mers & indexation

findere: simple strategy for speeding up queries and for reducing false positive calls from any Approximate Membership Query data structure.
- fimpera extends findere adding the abundance information.
kmtricks: modular tool suite for counting kmers, and constructing Bloom filters or kmer matrices, for large collections of sequencing data.
kmindex is a tool for indexing and querying sequencing samples. It is built on top of kmtricks.
back to sequences: Find sequences (reads, unitigs, genes) related to a set of kmers in large datasets, in a matter of seconds.
Backpack Quotient Filter: k-mer indexing data structure with abundance
short read connector: Detect similar reads from potentially large read set
DSK: Count K-mer in sequences

Pangenome graph manipulation

Pancat: Pangenome Comparison and Analysis Toolkit
GFAGraphs: a Python library to handle pangenome graph files in GFA format.

Comparative metagenomics with k-mers

Simka and SimkaMin: Comparative metagenomics for large-scale datasets
Comparead & Commet: comparison of metagenomic datasets

Species and bacterial strains identification

ORI: software using long nanopore reads to identify bacteria present in a sample at the strain level
StrainFLAIR: STRAIN-level proFiLing using vArIation gRaph

General-purpose sequencing data manipulation

GASSST: long read mapper
Leon: short read compressor (now included in GATB-core)
Bloocoo: short read corrector
BCALM: Construct compacted de Bruijn graphs (unitigs)

Protein Structure

A_Purva: Contact Map Overlap solver
MD-Jeep: Distance Geometry solver
CSA: Comparative Structural Alignment

Workflow

SLICEE: parallel execution of bioinformatics workflows

Comparative Genomics

CASSIS: detection of rearrangement breakpoints
PLAST: intensive bank-to-bank sequence comparison
DRJBreakpointFinder: detection and precise localization of excision sites in proviral segments

Pilon

Rahul Nayak — Mon, 08 Feb 2016 15:56:18 -0600

Pilon is a software tool which can be used to:

Automatically improve draft assemblies
Find variation among strains, including large event detection

Pilon requires as input a FASTA file of the genome along with one or more BAM files of reads aligned to the input FASTA file. Pilon uses read alignment analysis to identify inconsistencies between the input genome and the evidence in the reads. It then attempts to make improvements to the input genome, including:

Single base differences
Small indels
Larger indel or block substitution events
Gap filling
Identification of local misassemblies, including optional opening of new gaps

More at https://github.com/broadinstitute/pilon/wiki

Address of the bookmark: https://github.com/broadinstitute/pilon/wiki

Easyfig

Poonam Mahapatra — Fri, 29 Apr 2016 05:49:39 -0500

Easyfig has moved to github, for newer releases of Easyfig please visit our new webpage - https://mjsull.github.io/Easyfig. Easyfig is a Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface (GUI).

More at http://easyfig.sourceforge.net/

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

RACA: Reference-Assisted Chromosome Assembly

Priya Singh — Wed, 06 Apr 2016 09:29:50 -0500

Rreference-Assisted Chromosome Assembly (RACA), an algorithm to reliably order and orient sequence scaffolds generated by NGS and assemblers into longer chromosomal fragments using comparative genome information and paired-end reads.

http://www.ncbi.nlm.nih.gov/pubmed/23307812

http://bioen-compbio.bioen.illinois.edu/RACA/

Address of the bookmark: http://bioen-compbio.bioen.illinois.edu/RACA/