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

McClintock: Meta-pipeline to identify transposable element insertions using next generation sequencing data

BioStar — Tue, 27 Oct 2020 00:21:18 -0500

an integrated bioinformatics pipeline for the detection of TE insertions in whole-genome shotgun data, called McClintock (https://github.com/bergmanlab/mcclintock), which automatically runs and standardizes output for multiple TE detection methods. We demonstrate the utility of McClintock by evaluating six TE detection methods using simulated and real genome data from the model microbial eukaryote, Saccharomyces cerevisiae.

Address of the bookmark: https://github.com/bergmanlab/mcclintock

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

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

karyoploteR: plot whole genomes with arbitrary data

Abhimanyu Singh — Fri, 02 Feb 2018 03:24:28 -0600

karyoploteR is an R package to create karyoplots, that is, representations of whole genomes with arbitrary data plotted on them. It is inspired by the R base graphics system and does not depend on other graphics packages. The aim of karyoploteR is to offer the user an easy way to plot data along the genome to get broad genome-wide view to facilitate the identification of genome wide relations and distributions.

Address of the bookmark: https://bernatgel.github.io/karyoploter_tutorial/

Scripts for the analysis of HGT in genome sequence data.

Jit — Wed, 29 Nov 2017 16:44:10 -0600

Scripts for the analysis of HGT in genome sequence data

Address of the bookmark: https://github.com/reubwn/hgt

Epiviz: an interactive visualization tool for functional genomics data.

Jit — Mon, 09 Jul 2018 05:27:39 -0500

Epiviz is an interactive visualization tool for functional genomics data. It supports genome navigation like other genome browsers, but allows multiple visualizations of data within genomic regions using scatterplots, heatmaps and other user-supplied visualizations. It also includes data from the Gene Expression Barcode project for transcriptome visualization. It has a flexible plugin framework so users can addd3 visualizations. You can see a video tour here.

https://bioconductor.org/packages/release/bioc/html/epivizr.html

https://github.com/epiviz

https://github.com/epiviz/epiviz

Address of the bookmark: https://epiviz.github.io/

BamView: a free interactive display of read alignments in BAM data files

Neel — Fri, 09 Nov 2018 13:43:22 -0600

To run the application on UNIX from the downloaded jar file run the UNIX:

java -mx512m -jar BamView.jar

and extra command line options are given when '-h' is used:

java -jar BamView.jar -h

BAM files can be specified on the command line with the '-a' option:

java -mx512m -jar BamView.jar -a pathToFile/sorted.bam

If a BAM filename is not given on the command line BamView will prompt for a file to be entered. The BAM index file should have the same name as the BAM file but with a '.bai' suffix. Multiple BAM files can be loaded and overlaid in the viewer. To make this easier BamView will read in files that contain a list of filenames.

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

ZENBU: a collaborative, omics data integration and interactive visualization system

BioJoker — Fri, 04 Jan 2019 13:35:26 -0600

ZENBU is a data integration, data analysis, and visualization system enhanced for RNAseq, ChipSeq, CAGE and other types of next-generation-sequence-tag (NGS) based data. ZENBU allows for novel data exploration through "on-demand" data processing and interactive linked-visualizations and is able to make many-views from the same primary sequence alignment data which users can uploaded from BAM, BED, GFF and tab-text files.
Please check our documentation wiki for details on how to use the system, or check out some of the views above.

Address of the bookmark: http://fantom.gsc.riken.jp/zenbu/

OMTools: a software package for visualizing and processing optical mapping data

BioJoker — Fri, 29 Mar 2019 01:21:54 -0500

OMTools, an efficient and intuitive data processing and visualization suite to handle and explore large-scale optical mapping profiles. OMTools includes modules for visualization (OMView), data processing and simulation. These modules together form an accessible and convenient pipeline for optical mapping analyses.

https://github.com/TF-Chan-Lab/OMTools

Address of the bookmark: https://github.com/TF-Chan-Lab/OMTools