BOL: Related items

HASLR: a tool for rapid genome assembly of long sequencing reads

LEGE — Fri, 31 Jan 2020 05:50:15 -0600

HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation Sequencing reads (such as Illumina) from the same sample.

Address of the bookmark: https://github.com/vpc-ccg/haslr

GraphMap - A highly sensitive and accurate mapper for long, error-prone reads

Jit — Wed, 07 Jun 2017 04:18:16 -0500

GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html

Features

    Mapping position agnostic to alignment parameters.
    Consistently very high sensitivity and precision across different error profiles, rates and sequencing technologies even with default parameters.
    Circular genome handling to resolve coverage drops near ends of the genome.
    E-value.
    Meaningful mapping quality.
    Various alignment strategies (semiglobal bit-vector and Gotoh, anchored).
    Overlapping of reads for de novo assembly.
    Transcriptome mapping through internal construction of a transcriptome from a given genomic reference and a GTF file.
    ...and much more.

GraphMap is also used as an overlapper in a new de novo genome assembly project called Ra (https://github.com/mariokostelac/ra-integrate).
Ra attempts to create de novo assemblies from raw nanopore and PacBio reads without requiring error correction, for which a highly sensitive overlapper is required.

Currently, development of a new spliced-alignment mode for mapping RNA-seq reads is under way.
Description of the current effort as well as how to reach the experimental implementation can be found here: doc/rnaseq.md.

Address of the bookmark: https://github.com/isovic/graphmap

WhatsHap: fast and accurate read-based phasing

Jit — Mon, 28 May 2018 09:52:16 -0500

WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads.

Features

Very accurate results (Martin et al., WhatsHap: fast and accurate read-based phasing)

Works well with Illumina, PacBio, Oxford Nanopore and other types of reads

It phases SNVs, indels and even “complex” variants (such as TCG → AGAA)

Pedigree phasing mode uses reads from related individuals (such as trios) to improve results and to reduce coverage requirements (Garg et al., Read-Based Phasing of Related Individuals).

WhatsHap is easy to install

It is easy to use: Pass in a VCF and one or more BAM files, get out a phased VCF. Supports multi-sample VCFs.

It produces standard-compliant VCF output by default

If desired, get output that is compatible with ReadBackedPhasing

Open Source (MIT license)

Address of the bookmark: https://whatshap.readthedocs.io/en/latest/

CLARK: Fast, accurate and versatile sequence classification system

Jit — Sat, 15 Feb 2020 01:49:01 -0600

CLARK, a method based on a supervised sequence classification using discriminative k-mers. Considering two distinct specific classification problems (see the article for details), namely (1) the taxonomic classification of metagenomic reads to known bacterial genomes, and (2) the assignment of BAC clones and transcript to chromosome arms/centromeres (in the absence of a finished assembly for the reference genome), CLARK outperforms in classification speed and precision the best state-of-the-art methods.

http://clark.cs.ucr.edu/Spaced/

Address of the bookmark: http://clark.cs.ucr.edu/Spaced/

HELIANO: A fast and accurate tool for detection of Helitron-like elements

LEGE — Tue, 13 Aug 2024 07:16:34 -0500

Helitron-like elements (HLE1 and HLE2) are DNA transposons. They have been found in diverse species and seem to play significant roles in the evolution of host genomes. Although known for over twenty years, Helitron sequences are still challenging to identify. Here, we propose HELIANO (Helitron-like elements annotator) as an efficient solution for detecting Helitron-like elements.

https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae679/7730539?login=true

Address of the bookmark: https://github.com/Zhenlisme/heliano/

MashMap: a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to reference genome(s)

Jit — Tue, 12 Dec 2017 17:23:31 -0600

MashMap is a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to reference genome(s). It maps a query sequence against a reference region if and only if its estimated alignment identity is above a specified threshold. It does not compute the alignments explicitly, but rather estimates a k-mer based Jaccard similarity using a combination of Winnowing and MinHash. This is then converted to an estimate of sequence identity using the Mash distance. An appropriate k-mer sampling rate is automatically determined given minimum local alignment length and identity thresholds. The efficiency of the algorithm improves as both of these thresholds are increased.

Address of the bookmark: https://github.com/marbl/MashMap

gSearch: a fast and flexible general search tool for whole-genome sequencing

Jit — Mon, 06 Aug 2018 17:19:15 -0500

gSearch compares sequence variants in the Genome Variation Format (GVF) or Variant Call Format (VCF) with a pre-compiled annotation or with variants in other genomes. Its search algorithms are subsequently optimized and implemented in a multi-threaded manner.

Address of the bookmark: http://ml.ssu.ac.kr/gSearch/index.html

ANItools web: a web tool for fast genome comparison within multiple bacterial strains

Jit — Wed, 14 Nov 2018 04:34:23 -0600

ANItools is a software package written by PERL scripts that can be run in a Linux/Unix system. If you want to compare bacterial genomes and calculate their average nucleotide identity (ANI), you could download and run this program directly. Or you could send us the genome sequence by email. Then we will do the analysis work for you.

https://academic.oup.com/database/article/doi/10.1093/database/baw084/2630454

Address of the bookmark: http://ani.mypathogen.cn/

mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

Jit — Wed, 13 Nov 2019 22:20:19 -0600

mosdepth can output:

per-base depth about 2x as fast samtools depth--about 25 minutes of CPU time for a 30X genome.
mean per-window depth given a window size--as would be used for CNV calling.
the mean per-region given a BED file of regions.
a distribution of proportion of bases covered at or above a given threshold for each chromosome and genome-wide.
quantized output that merges adjacent bases as long as they fall in the same coverage bins e.g. (10-20)
threshold output to indicate how many bases in each region are covered at the given thresholds.
A summary of mean depths per chromosome and within specified regions per chromosome.

Address of the bookmark: https://github.com/brentp/mosdepth

chromeister: An ultra fast, heuristic approach to detect conserved signals in extremely large pairwise genome comparisons.

Jit — Thu, 03 Feb 2022 04:01:55 -0600

chromeister: An ultra fast, heuristic approach to detect conserved signals in extremely large pairwise genome comparisons.

USAGE:

-query: sequence A in fasta format
-db: sequence B in fasta format
-out: output matrix
-kmer Integer: k>1 (default 32) Use 32 for chromosomes and genomes and 16 for small bacteria
-diffuse Integer: z>0 (default 4) Use 4 for everything - if using large plant genomes you can try using 1
-dimension Size of the output matrix and plot. Integer: d>0 (default 1000) Use 1000 for everything that is not full genome size, where 2000 is recommended

Address of the bookmark: https://github.com/estebanpw/chromeister