BOL: Related items

LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data

BioStar — Tue, 18 Feb 2020 03:24:22 -0600

LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or base/indel alignment uncertainty), which are usually ignored by other methods or only used for filtering.

https://github.com/CSB5/lofreq

http://csb5.github.io/lofreq/installation/

https://github.com/CSB5/lofreq/tree/master/dist

Address of the bookmark: http://csb5.github.io/lofreq/

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

The complete sequence of a human genome

Neel — Thu, 31 Mar 2022 23:58:18 -0500

The completed regions include all centromeric satellite arrays, recent segmental duplications, and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies.

Address of the bookmark: https://www.science.org/doi/10.1126/science.abj6987

Seal: SEquence ALignment evaluation suite

Jit — Wed, 03 Jan 2018 05:05:46 -0600

Seal is a comprehensive sequencing simulation and alignment tool evaluation suite. This software (implemented in Java) provides several utilities that can be used to evaluate alignment algorithms, including:

Reading a pre-existing reference genome from one or more FASTA files.
Alternatively, generating an artificial reference genome based on input parameters (length, repeat count, repeat length, repeat variability rate).
Simulating reads from random locations in the genome based on input parameters of read length, coverage, sequencing error rate, and indel rate.
Applying alignment tools to the genome and the reads through a standardized interface.
Parsing the output of the alignment tool and calculating the number of reads that were correctly or incorrectly mapped.
Computing run times and measures of accuracy.

Seal has interfaces to evaluate the following software packages:

Bowtie
BWA
MAQ
mrFAST
mrsFAST
Novoalign
SHRiMP
SOAPv2

Address of the bookmark: http://compbio.case.edu/seal/

NGS Tutorial

Jit — Mon, 05 Sep 2016 09:50:46 -0500

These tutorials are written for hundreds of bioinformaticians trying to cope with large volume of next-generation sequencing (NGS) data. NGS technologies brought a dramatic shift in the world of sequencing. Merely five years back, genome sequencing of higher eukaryotes used to be very expensive endeavor. To get a genome of interest sequenced, hundreds of scientists had to raise funds together by writing a joint white-paper and petitioning to various government agencies. The tasks of sequencing and assembly were handled by dedicated sequencing facilities, of which only a few existed around the globe. Naturally, the capacities at those sequencing facilities were significantly constrained from high volume of requests

Address of the bookmark: http://www.homolog.us/Tutorials/index.php

DISCO : multi threaded and multiprocess distributed memory overlap-layout-consensus (OLC) metagenome assembler

Jit — Mon, 10 Jul 2017 10:09:27 -0500

DISCO is a multi threaded and multiprocess distributed memory overlap-layout-consensus (OLC) metagenome assembler. Disco was developed as a scalable assembler to assemble large metagenomes from billions of Illumina sequencing reads of complex microbial communities. Disco was parallelized for computer clusters in a hybrid architecture that integrated shared-memory multi-threading, point-to-point message passing, and remote direct memory access. The assembly and scaffolding were performed using an iterative overlap graph approach.

Address of the bookmark: http://disco.omicsbio.org/

Metassembler: merging and optimizing de novo genome assemblies

Rahul Nayak — Tue, 08 May 2018 04:52:33 -0500

Metassembler combines multiple whole genome de novo assemblies into a combined consensus assembly using the best segments of the individual assemblies.

Genome assembly projects typically run multiple algorithms in an attempt to find the single best assembly, although those assemblies often have complementary, if untapped, strengths and weaknesses. We present our metassembler algorithm that merges multiple assemblies of a genome into a single superior sequence.

Address of the bookmark: https://sourceforge.net/projects/metassembler/?source=directory

ARC: pipeline which facilitates iterative, reference guided de novo assemblies

Jit — Thu, 26 Jul 2018 09:20:26 -0500

ARC is a pipeline which facilitates iterative, reference guided de novo assemblies with the intent of:

Reducing time in analysis and increasing accuracy of results by only considering those reads which should assemble together.
Reducing/removing reference bias as compared to mapping based approaches.

The software is designed to work in situations where a whole-genome assembly is not the objective, but rather when the researcher wishes to assemble discreet 'targets' contained within next-generation shotgun sequence data. ARC decomplexifies the traditionally difficult problem of assembly by breaking the reads into small, manageable subsets which can then be assembled quickly and efficiently in parallel. Applications include those in which the researcher wishes to de novo assemble specific content and a set of semi-similar reference targets is available to initialize the assembly process.

https://ibest.github.io/ARC/

Address of the bookmark: https://ibest.github.io/ARC/

NovoGraph: building whole genome graphs from long-read-based de novo assemblies

Jit — Thu, 15 Nov 2018 12:48:30 -0600

NovoGraph: building whole genome graphs from long-read-based de novo assemblies

An algorithmically novel approach to construct a genome graph representation of long-read-based de novo sequence assemblies. We then provide a proof of principle by creating a genome graph of seven ethnically-diverse human genomes.

https://f1000research.com/articles/7-1391/v1

Address of the bookmark: https://github.com/NCBI-Hackathons/NovoGraph

ECTOOLS: Long Read Correction and other Correction tools

Jit — Fri, 05 Jan 2018 04:02:22 -0600

Long Read Correction and other Correction tools

This package is a loose collection of scripts. To run the correction
routine see the section below. Descriptions of the other scripts
are at the bottom of this file.

Contact: gurtowsk@cshl.edu

In short, the correction algorithm takes as input the unitigs from a short read assembly and uses them to correct long read data. More background information for the algorithm can be found:
http://schatzlab.cshl.edu/presentations/2013-06-18.PBUserMeeting.pdf

Address of the bookmark: https://github.com/jgurtowski/ectools