BOL: Related items

ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information

BioJoker — Sun, 20 Jan 2019 06:34:36 -0600

ClipCrop for detecting SVs with single-base resolution using soft-clipping information. A soft-clipped sequence is an unmatched fragment in a partially mapped read. To assess the performance of ClipCrop with other SV-detecting tools, we generated various patterns of simulation data – SV lengths, read lengths, and the depth of coverage of short reads – with insertions, deletions, tandem duplications, inversions and single nucleotide alterations in a human chromosome.

Address of the bookmark: https://github.com/shinout/clipcrop

EFS: an ensemble feature selection tool implemented as R-package and web-application

Jit — Tue, 28 Jan 2020 05:12:23 -0600

The software EFS (Ensemble Feature Selection) makes use of multiple feature selection methods and combines their normalized outputs to a quantitative ensemble importance. Currently, eight different feature selection methods have been integrated in EFS, which can be used separately or combined in an ensemble.

https://biodatamining.biomedcentral.com/articles/10.1186/s13040-017-0142-8

Address of the bookmark: http://efs.heiderlab.de/

truvari: Structural variant comparison tool for VCFs

Jit — Tue, 30 Jun 2020 21:30:44 -0500

Structural variant comparison tool for VCFs

Given benchmark and comparsion sets of SVs, calculate the recall, precision, and f-measure.

Spiral Genetics

Motivation

Address of the bookmark: https://github.com/spiralgenetics/truvari

VICUNA: a software tool that enables consensus assembly of ultra-deep sequence derived from diverse viral or other heterogeneous populations.

biogeek — Tue, 25 Aug 2020 03:40:17 -0500

VICUNA is a de novo assembly program targeting populations with high mutation rates. It creates a single linear representation of the mixed population on which intra-host variants can be mapped. For clinical samples rich in contamination (e.g., >95%), VICUNA can leverage existing genomes, if available, to assemble only target-alike reads. After initial assembly, it can also use existing genomes to perform guided merging of contigs. For each data set (e.g., Illumina paired read, 454), VICUNA outputs consensus sequence(s) and the corresponding multiple sequence alignment of constituent reads. VICUNA efficiently handles ultra-deep sequence data with tens of thousands fold coverage.

http://software.broadinstitute.org/viral/docs/vicuna_v1.0.pdf

Address of the bookmark: https://www.broadinstitute.org/viral-genomics/vicuna

JumboDB: tool for de Bruijn graph construction

BioStar — Tue, 17 Aug 2021 13:33:46 -0500

jumboDB tool for fast de Bruijn graph construction from long sequences (reads or genomes) with very low error rate. JumboDB is not a genome assembler by itself but rather a subroutine that translates a set of reads into compressed de Bruijn graph.

More at https://github.com/AntonBankevich/jumboDB

Address of the bookmark: https://github.com/AntonBankevich/jumboDB

A web-based tool for sequence alignment statistics and innovative visualization

BioStar — Thu, 04 Apr 2024 01:44:50 -0500

AlignStatPlot, a new R package and online tool that is well-documented and easy-to usefor MSA and post-MSA analysis. This tool performs both traditional and cutting-edge analy-ses on sequencing data and generates new visualisation methods for MSA results. Whencompared to currently available tools, AlignStatPlot provides a robust ability to handle andvisualise diversity data, while the online version will save time and encourage researchersto focus on explaining their findings. It is a simple tool that can be used in conjunction withpopulation genetics software (PDF) AlignStatPlot: An R package and online tool for robust sequence alignment statistics and innovative visualization of big data.

Address of the bookmark: https://bioinformatics.um6p.ma/AlignStatPlot/

Jaeger : an accurate and fast deep-learning tool to detect bacteriophage sequences

LEGE — Sun, 31 Aug 2025 06:30:16 -0500

Jaeger is a tool that utilizes homology-free machine learning to identify phage genome sequences that are hidden within metagenomes. It is capable of detecting both phages and prophages within metagenomic assemblies.

Address of the bookmark: https://github.com/MGXlab/Jaeger

npScarf: Scaffolding and Completing Assemblies in Real-time Fashion

Jit — Tue, 23 May 2017 04:53:29 -0500

npScarf (jsa.np.npscarf) is a program that scaffolds and completes draft genomes assemblies in real-time with Oxford Nanopore sequencing. The pipeline can run on a computing cluster as well as on a laptop computer for microbial datasets. It also facilitates the real-time analysis of positional information such as gene ordering and the detection of genes from mobile elements (plasmids and genomic islands).

Complete paper at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5321748/

Address of the bookmark: https://github.com/mdcao/npScarf

WAAFLE: a Workflow to Annotate Assemblies and Find LGT Events.

Neel — Thu, 23 Sep 2021 14:31:06 -0500

Lateral gene transfer (LGT) is an important mechanism for genome diversification in microbial communities, including the human microbiome. While methods exist to identify LGTs from sequenced isolate genomes, identifying LGTs from community metagenomes remains an open problem. To address this, we developed WAAFLE: a Workflow to Annotate Assemblies and Find LGT Events.

Address of the bookmark: http://huttenhower.sph.harvard.edu/waafle

MIX: Combining multiple assemblies from NGS data

Rahul Nayak — Tue, 08 May 2018 04:58:05 -0500

Mix is a tool that combines two or more draft assemblies, without relying on a reference genome and has the goal to reduce contig fragmentation and thus speed-up genome finishing. The proposed algorithm builds an extension graph where vertices represent extremities of contigs and edges represent existing alignments between these extremities. These alignment edges are used for contig extension. The resulting output assembly corresponds to a path in the extension graph that maximizes the cumulative contig length.

The Mix algorithm, approach and results were published in BMC bioinformatics : http://www.biomedcentral.com/1471-2105/14/S15/S16.

Address of the bookmark: https://github.com/cbib/MIX