BOL: Related items

Minda: a tool for evaluating structural variant (SV) callers

LEGE — Sun, 31 Mar 2024 02:43:50 -0500

Minda is a tool for evaluating structural variant (SV) callers that

standardizes VCF records for compatibility with both germline and somatic SV callers,
benchmarks against a single VCF input file, or
benchmarks against an ensemble call set created from multiple VCF input files.

Address of the bookmark: https://github.com/KolmogorovLab/minda

LoVis4u: Locus Visualisation tool for comparative genomics

LEGE — Tue, 17 Sep 2024 02:30:57 -0500

Description

LoVis4u is a bioinformatics tool for Loci Visualisation.

LoVis4u, a command-line tool and Python API designed for highly customizable and fast visualisation of multiple genomic loci. LoVis4u generates vector images in PDF format based on annotation data from GenBank or GFF files. It is capable of visualising entire genomes of bacteriophages as well as plasmids and user-defined regions of longer prokaryotic genomes. Additionally, LoVis4u offers optional data processing steps to identify and highlight accessory and core genes in input sequences.

https://art-egorov.github.io/lovis4u/

Address of the bookmark: https://github.com/art-egorov/lovis4u

Unicycler: Hybrid assembly pipeline for bacterial genomes

Jit — Fri, 10 Nov 2017 03:58:27 -0600

Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs a miniasm+Racon pipeline. For the best possible assemblies, give it both Illumina reads and long reads, and it will conduct a hybrid assembly.

Address of the bookmark: https://github.com/rrwick/Unicycler

BakRep (Denglish blend of Bakterien & Repository) simplifies access to this data

Neel — Wed, 13 Aug 2025 02:31:28 -0500

2,438,386 bacterial genomes at your fingertips consistently processed & characterized, enriched with metadata, accessible via a flexible search engine.

BakRep (Denglish blend of Bakterien & Repository) simplifies access to this data. It integrates enriched genomic information with metadata accessible via a flexible search-engine.

Key features

Assembly statistics: ensure data quality with genome-based key metrics
Taxonomic classification: robust, purely genome-based classifications (GTDB)
MLST: subtyping for deeper insights into genetic variation
Annotation: comprehensive & taxonomy-independent (Bakta)
Metadata: full original submission records

Address of the bookmark: https://bakrep.computational.bio/

PeGAS: A Comprehensive Bioinformatic Solution for Pathogenic Bacterial Genomic Analysis

LEGE — Mon, 01 Sep 2025 01:18:10 -0500

This is PeGAS, a powerful bioinformatic tool designed for the seamless quality control, assembly, and annotation of Illumina paired-end reads specific to pathogenic bacteria. This tool integrates state-of-the-art open-source software to provide a streamlined and efficient workflow, ensuring accurate insights into the genomic makeup of pathogenic microbial strains.

Address of the bookmark: https://github.com/liviurotiul/PeGAS

GMASS: a novel measure for genomeassembly structural similarity

Abhimanyu Singh — Sun, 14 Apr 2019 20:35:40 -0500

The GMASS score is a novel measure for representing structural similarity between two assemblies. It will contribute to the understanding of assembly output and developing de novo assemblers.

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2710-z

Address of the bookmark: http://bioinfo.konkuk.ac.kr/GMASS/htdocs/syncircos.php

Reference-free prediction of rearrangement breakpoint reads

Neel — Thu, 08 Mar 2018 05:05:25 -0600

lideSort-BPR ( b reak p oint r eads) is based on a fast algorithm for all-against-all comparisons of short reads and theoretical analyses of the number of neighboring reads. When applied to a dataset with a sequencing depth of 100×, it finds ∼88% of the breakpoints correctly with no false-positive reads. Moreover, evaluation on a real prostate cancer dataset shows that the proposed method predicts more fusion transcripts correctly than previous approaches, and yet produces fewer false-positive reads. To our knowledge, this is the first method to detect breakpoint reads without using a reference genome.

https://github.com/ewijaya/slidesort-bpr

Address of the bookmark: https://code.google.com/archive/p/slidesort-bpr/

MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads

Rahul Nayak — Fri, 11 May 2018 05:07:45 -0500

MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads. MECAT employs novel alignment and error correction algorithms that are much more efficient than the state of art of aligners and error correction tools. MECAT can be used for effectively de novo assemblying large genomes. For example, on a 32-thread computer with 2.0 GHz CPU , MECAT takes 9.5 days to assemble a human genome based on 54x SMRT data, which is 40 times faster than the current PBcR-Mhap pipeline. MECAT performance were compared with PBcR-Mhap pipeline, FALCON and Canu(v1.3) in five real datasets. The quality of assembled contigs produced by MECAT is the same or better than that of the PBcR-Mhap pipeline and FALCON.

https://www.nature.com/articles/nmeth.4432

Address of the bookmark: https://github.com/xiaochuanle/MECAT

Jvarkit : Java utilities for Bioinformatics

Jit — Fri, 08 Jun 2018 09:31:55 -0500

Collection of Java tool kits for bioinformatics works: Jvarkit : Java utilities for Bioinformatics

Address of the bookmark: http://lindenb.github.io/jvarkit/

GenomeMapper: Simultaneous alignment of short reads against multiple genomes

Jit — Fri, 25 May 2018 09:29:44 -0500

GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. It can be used to align against multiple genomes simulanteously or against a single reference. If you are unsure which one is the appropriate GenomeMapper, you might want to use the latter https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2768987/

Address of the bookmark: http://1001genomes.org/software/genomemapper.html