BOL: Related items

Referee: Genome assembly quality scores

Jit — Sun, 04 Nov 2018 16:44:30 -0600

Modern genome sequencing technologies provide a succint measure of quality at each position in every read, however all of this information is lost in the assembly process. Referee summarizes the quality information from the reads that map to a site in an assembled genome to calculate a quality score for each position in the genome assembly.

We accomplish this by first calculating genotype likelihoods for every site. For a given site in a diploid genome, there are 10 possible genotypes (AA, AC, AG, AT, CC, CG, CT, GG, GT, TT). Referee takes as input the genotype likelihoods calculated for all 10 genotypes given the called reference base at each position.

Referee is a program to calculate a quality score for every position in a genome assembly. This allows for easy filtering of low quality sites for any downstream analysis.

https://github.com/gwct/referee

Address of the bookmark: https://gwct.github.io/referee/#

Evaluation of genome assembly software based on long reads

BioStar — Fri, 01 Feb 2019 11:55:54 -0600

TGS technologies have been used to produce highly accurate de novo assemblies of hundreds of microbial genomes and highly contiguous reconstructions of many dozens of plant and animal genomes, enabling new insights into evolution and sequence diversity. They have also been applied to resequencing analyses, to create detailed maps of structural variations in many species. Also, these new technologies have been used to fill in many of the gaps in the human reference genome.

In this report, we compare and evaluate several genome assembly software based on TSG technology. The experimentation has been performed on 4 reference genomes and the results evaluated with the QUAST software. The 11 software that have been evaluated are: Celera Assembler , Falcon , Miniasm, Newbler , SGA Assembler, Smartdenovo, Abruijn, Ra, DBG2OLC, Spades and Cerulean. The first 8 software use only long reads, while the 3 last software can merge long and short reads

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

RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes

Rahul Nayak — Fri, 01 May 2020 03:00:40 -0500

RefKA, a reference-based approach for long read genome assembly. This approach relies on breaking up a closely related reference genome into bins, aligning k-mers unique to each bin with PacBio reads, and then assembling each bin in parallel followed by a final bin-stitching step.

Address of the bookmark: https://github.com/AppliedBioinformatics/RefKA

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

LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data

Neel — Wed, 23 Jun 2021 07:54:53 -0500

LoReTTA (Long Read Template-Targeted Assembler), a tool designed for performing de novo assembly of long reads generated from viral genomes on the PacBio platform. LoReTTA exploits a reference genome to guide the assembly process, an approach that has been successful with short reads.

https://academic.oup.com/ve/article/7/1/veab042/6248116

Address of the bookmark: https://academic.oup.com/ve/article/7/1/veab042/6248116

The Genome 10K Project

Tue, 29 Jul 2014 09:11:04 -0500

https://genome10k.soe.ucsc.edu The Genome 10K project aims to assemble a genomic zoo—a collection of DNA sequences representing the genomes of 10,000 vertebrate species, approximately one for every vertebrate genus. The trajectory of cost reduction in DNA sequencing suggests that this project will be feasible within a few years. Capturing the genetic diversity of vertebrate species would create an unprecedented resource for the life sciences and for worldwide conservation efforts. The growing Genome 10K Community of Scientists (G10KCOS), made up of leading scientists representing major zoos, museums, research centers, and universities around the world, is dedicated to coordinating efforts in tissue specimen collection that will lay the groundwork for a large-scale sequencing and analysis project.

Redundans

Jit — Thu, 01 Sep 2016 08:28:11 -0500

Redundans pipeline assists an assembly of heterozygous genomes.
Program takes as input assembled contigs, paired-end and/or mate pairs sequencing libraries and returns scaffolded homozygous genome assembly, that should be less fragmented and with total size smaller than the input contigs. In addition, Redundans will automatically close the gaps resulting from genome assembly or scaffolding more details.

The pipeline consists of three steps/modules:

redundancy reduction: detection and selectively removal of redundant contigs from an initial de novo assembly
scaffolding: joining of genome fragments using paired-end and/or mate-pairs reads
gap closing

Redundans is:

fast & lightweight, multi-core support and memory-optimised, so it can be run even on the laptop for small-to-medium size genomes
flexible toward many sequencing technologies (Illumina, 454 or Sanger) and library types (paired-end, mate pairs, fosmids)
modular: every step can be ommited or replaced by another tools

Address of the bookmark: https://github.com/Gabaldonlab/redundans

Standardized velvet assembly report

Poonam Mahapatra — Fri, 09 Dec 2016 03:59:59 -0600

Requirements:

velvet (velveth velvetg should be in your PATH)
R (with Sweave)
pdflatex (usually part of TeTeX)
ggplot2 (from R prompt type install.packages("ggplot2","proto","xtable"))
Perl

Optional:

BLAT or BLAST (to generate alignments against a reference genome). If using BLAT, add faToTwoBit,gfClient,gfServer to your PATH. If using BLAST, add blastall and formatdb.

Edit permute.sh to your liking, paying particular attention to the kmer, cvCut, expCov, and other flags

To Run:

perl fastaAllSize mysequences.fa > mysequences.stat or gunzip -c mysequences.fa.gz | fastaAllSize > mysequences.stat Substitute fastqAllSize for fastq files.
./permute.sh mysequences (leave out the .fa)

https://github.com/leipzig/standardized-velvet-assembly-report

Address of the bookmark: https://github.com/leipzig/standardized-velvet-assembly-report

ScaffMatch

Jit — Tue, 13 Dec 2016 10:23:56 -0600

caffMatch is a novel scaffolding tool based on Maximum-Weight Matching able to produce high-quality scaffolds from NGS data (reads and contigs). The tool is written in Python 2.7. It also includes a bash script wrapper that calls aligner in case one needs to first map reads to contigs (instead of providing .sam files).

The arguments accepted by ScaffMatch are:

-w) Working directory -- this is the directory where ScaffMatch files are stored. These are .sam files produced after mapping reads to contigs and the resulting scaffolds file `scaffolds.fa` fasta file;

-c) Contig fasta file;

-m) Command line argument with no options. It is used when .sam files are used instead of reads .fastq files. Do not use this option if you provide reads files;

-1) (Comma separated list of) either .fastq or .sam file(s) corresponding to the first read of the read pair;

-2) (Comma separated list of) either .fastq or .sam file(s) corresponding to the second read of the read pair;

-i) (Comma separated list of) insert size(s) of the library(-ies);

-s) (Comma separated list of) library(-ies) standard deviation(s) of insert size(s);

-t) Bundle threshold. Pairs of contigs supported by number of read pairs less than the value of this argument are discarded. Optional argument, by default it is equal to 5;

-g) Matching heuristics: use `max_weight` for Maximum Weight Matching heuristics with the Insertion step, use `backbone` for Maximum Weight Matching heuristics without the Insertion step, use `greedy` for Greedy Matching heuristics;

-l) Log file - where to store the logs. Optional argument. By default, stdout is used.

Address of the bookmark: http://alan.cs.gsu.edu/NGS/?q=content/scaffmatch