BOL: Related items

VariantBam: Filtering and profiling of next-generational sequencing data using region-specific rules

Rahul Nayak — Thu, 04 Oct 2018 16:30:44 -0500

VariantBam is a tool to extract/count specific sets of sequencing reads from next-generational sequencing files. To save money, disk space and I/O, one may not want to store an entire BAM on disk. In many cases, it would be more efficient to store only those read-pairs or reads who intersect some region around the variant locations. Alternatively, if your scientific question is focused on only one aspect of the data (e.g. breakpoints), many reads can be removed without losing the information relevant to the problem.

Address of the bookmark: https://github.com/broadinstitute/VariantBam

EXCAVATOR: detecting copy number variants from whole-exome sequencing data

Radha Agarkar — Fri, 04 Jan 2019 10:10:48 -0600

EXCAVATOR, for the detection of copy number variants (CNVs) from whole-exome sequencing data. EXCAVATOR combines a three-step normalization procedure with a novel heterogeneous hidden Markov model algorithm and a calling method that classifies genomic regions into five copy number states. We validate EXCAVATOR on three datasets and compare the results with three other methods. These analyses show that EXCAVATOR outperforms the other methods and is therefore a valuable tool for the investigation of CNVs in largescale projects, as well as in clinical research and diagnostics. EXCAVATOR is freely available at http://sourceforge.net/projects/excavatortool/.

EXCAVATOR is a novel software package for the detection of copy number variants (CNVs) from whole-exome sequencing data.
EXCAVATOR has been published on Genome Biology (http://genomebiology.com/2013/14/10/R120/abstract).

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

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/

FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads

Jit — Tue, 28 Jan 2020 03:27:33 -0600

FastGT is a program package for whole-genome genotyping of genome variants directly from raw sequencing reads. It is written in C and runs in Linux. FastGT uses a list of variant-specific k-mer pairs that are unique in human genome, counts the frequency of k-mers in sequencing data and predicts the genotype. All this takes less than 1 hour on average low-cost Linux server.

http://bioinfo.ut.ee/FastGT/

https://github.com/bioinfo-ut/GenomeTester4/

Address of the bookmark: http://bioinfo.ut.ee/FastGT/

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

AccessSyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies

Jit — Sat, 01 Feb 2020 13:38:49 -0600

AccessSyRI: finding genomic rearrangements andlocal sequence differences from whole-genome assemblies

SyRI, a pairwise whole-genome comparison tool for chromosome-level assemblies. SyRI starts by finding rearranged regions and then searches for differences in the sequences, which are distinguished for residing in syntenic or rearranged regions. This distinction is important as rearranged regions are inherited differently compared to syntenic regions.

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1911-0

Address of the bookmark: https://github.com/schneebergerlab/syri

doubletrouble: identify duplicated genes from whole-genome protein sequences and classify

LEGE — Tue, 05 Mar 2024 00:23:49 -0600

doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The duplication modes are i. segmental duplication (SD); ii. tandem duplication (TD); iii. proximal duplication (PD); iv. transposed duplication (TRD) and; v. dispersed duplication (DD). Transposon-derived duplicates (TRD) can be further subdivided into rTRD (retrotransposon-derived duplication) and dTRD (DNA transposon-derived duplication). If users want a simpler classification scheme, duplicates can also be classified into SD- and SSD-derived (small-scale duplication) gene pairs. Besides classifying gene pairs, users can also classify genes, so that each gene is assigned a unique mode of duplication. Users can also calculate substitution rates per substitution site (i.e., Ka and Ks) from duplicate pairs, find peaks in Ks distributions with Gaussian Mixture Models (GMMs), and classify gene pairs into age groups based on Ks peaks.

Address of the bookmark: https://bioconductor.org/packages/release/bioc/html/doubletrouble.html

CoverM: Read coverage calculator for metagenomics

Neel — Thu, 29 Apr 2021 23:39:14 -0500

CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications.

CoverM calculates coverage of genomes/MAGs coverm genome (help) or individual contigs coverm contig (help). Calculating coverage by read mapping, its input can either be BAM files sorted by reference, or raw reads and reference genomes in various formats.

Address of the bookmark: https://github.com/wwood/CoverM

RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs

Jit — Sun, 27 Oct 2019 00:57:23 -0500

Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, Lippman ZB, Schatz MC: Fast and accurate reference-guided scaffolding of draft genomes. bioRxiv 2019.

RaGOO is a tool for coalescing genome assembly contigs into pseudochromosomes via minimap2 alignments to a closely related reference genome. The focus of this tool is on practicality and therefore has the following features:

Good performance. On a MacBook Pro using Arabidopsis data, pseudochromosome construction takes less than a minute and the whole pipeline with SV calling takes ~2 minutes.
Intact ordering and orienting of contigs.
Misassembly correction
GFF lift-over
Structural variant calling with and integrated version of Assemblytics
Confidence scores associated with the grouping, localization, and orientation for each contig.

Address of the bookmark: https://github.com/malonge/RaGOO

PLAST: A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool

Jit — Fri, 01 Dec 2017 04:10:54 -0600

PLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast suite of algorithms.

Relying on unique software architecture, PLAST takes full advantage of recent multi-core personal computers without requiring any additional hardware devices.

PLAST stands for Parallel Local Sequence Alignment Search Tool and is was published in BMC Bioinformatics.

PLAST is a general purpose sequence comparison tool providing the following benefits:

PLAST is a high-performance sequence comparison tool designed to compare two sets of sequences (query vs. reference),
Reduces the processing time of sequences comparisons while providing highest quality results,
Contains a fully integrated data filtering engine capable of selecting relevant hits with user-defined criteria (E-Value, identity, coverage, alignment length, etc.),
Does not require any additional hardware, since it is a software solution. It is easy to install, cost-effective, takes full advantage of multi-core processors and uses a small RAM footprint,
Ready to be used on desktop computer, cluster, cloud as well as within distributed system running Hadoop.

https://plast.inria.fr/

Address of the bookmark: https://plast.inria.fr/