BOL: Related items

NxRepair: error correction in de novo assemblies using Nextera Mate Pair Reads

BioStar — Thu, 24 Jan 2019 10:35:12 -0600

NxRepair is a python module that automatically detects large structural errors in de novo assemblies using Nextera mate pair reads. The decector will break a contig at the site of an identified misassembly and will generate a new fasta file containing both the corrected contigs and the correct, unaffected contigs.

https://nxrepair.readthedocs.io/en/latest/tutorial.html

nxrepair aligned_matepairs.bam assemblyfasta.fasta error_locations.csv new_fasta.fasta

Address of the bookmark: https://github.com/rebeccaroisin/nxrepair

RACA: Reference-Assisted Chromosome Assembly

Priya Singh — Wed, 06 Apr 2016 09:29:50 -0500

Rreference-Assisted Chromosome Assembly (RACA), an algorithm to reliably order and orient sequence scaffolds generated by NGS and assemblers into longer chromosomal fragments using comparative genome information and paired-end reads.

http://www.ncbi.nlm.nih.gov/pubmed/23307812

http://bioen-compbio.bioen.illinois.edu/RACA/

Address of the bookmark: http://bioen-compbio.bioen.illinois.edu/RACA/

DISCOVAR

Abhimanyu Singh — Mon, 18 Apr 2016 11:59:16 -0500

DISCOVAR is a new variant caller and DISCOVAR de novo a new genome assembler, both designed for state-of-the-art data. Their inputs are chosen to optimize quality while keeping costs low. Currently it takes as input Illumina reads of length 250 or longer — produced on MiSeq or HiSeq 2500 — and from a single PCR-free library. These data enable a level of completeness and continuity that was not previously possible.

DISCOVAR can call variants on a region by region basis, potentially tiling an entire large genome. DISCOVAR variant calling is under active development and transitioning to VCF.

DISCOVAR de novo can generate de novo assemblies for both large and small genomes. It currently does not call variants.

More at https://www.broadinstitute.org/software/discovar/blog/?page_id=14

Address of the bookmark: https://www.broadinstitute.org/software/discovar/blog/

splitbam: splits a BAM by chromosomes

Jit — Tue, 28 Feb 2017 09:01:28 -0600

splitbam splits a BAM by chromosomes.

Using the reference sequence dictionary (*.dict), it also creates some empty BAM files if no sam record was found for a chromosome. A pair of 'mock' SAM-Records can also be added to those empty BAMs to avoid some tools (like samtools) to crash.

Usage

java -jar splitbam.jar -p OUT/__CHROM__/__CHROM__.bam -R ref.fasta (bam|sam|stdin)

Options

-h help; This screen.
-R (indexed reference file) REQUIRED.
-u (unmapped chromosome name): default:Unmapped
-e | --empty : generate EMPTY bams for chromosome having no read mapped
-m | --mock : if option '-e', add a mock pair of sam records to the empty bam
-p (output file/bam pattern) REQUIRED. MUST contain __CHROM__ and end with .bam
-s assume input is sorted.
-x | --index create index.
-t | --tmp (dir) tmp file directory
-G (file) chrom-group file (see below)

Address of the bookmark: https://code.google.com/archive/p/jvarkit/wikis/SplitBam.wiki

DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies

Jit — Wed, 19 Apr 2017 10:09:51 -0500

DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies

Our work is published in Scientific Reports:

Ye, C. et al. DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies. Sci. Rep. 6, 31900; doi: 10.1038/srep31900 (2016).

http://www.nature.com/articles/srep31900

The manual can be downloaded from:

https://github.com/yechengxi/DBG2OLC/raw/master/Manual.docx

To use precompiled versions,please go to:

https://github.com/yechengxi/DBG2OLC/tree/master/compiled

Address of the bookmark: https://github.com/yechengxi/DBG2OLC

Flye: Fast and accurate de novo assembler for single molecule sequencing reads

Jit — Fri, 04 May 2018 19:16:22 -0500

Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies. The algorithm uses an A-Bruijn graph to find the overlaps between reads and does not require them to be error-corrected. After the initial assembly, Flye performs an extra repeat classification and analysis step to improve the structural accuracy of the resulting sequence. The package also includes a polisher module, which produces the final assembly of high nucleotide-level quality.

Address of the bookmark: https://github.com/fenderglass/Flye

LACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)

Jit — Mon, 14 May 2018 04:26:30 -0500

LACHESIS is method that exploits contact probability map data (e.g. from Hi-C) for chromosome-scale de novo genome assembly.

Further information about LACHESIS, including source code, documentation and a user's guide are available at: http://shendurelab.github.io/LACHESIS.

Manuscript describing LACHESIS was published as: Burton JN#, Adey A, Patwardhan RP, Qiu R, Kitzman JO, Shendure J#. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nature Biotechnology 2013 Dec;31(12):1119-25. doi: 10.1038/nbt.272. PubMed PMID: 24185095.

http://shendurelab.github.io/LACHESIS/

Address of the bookmark: http://shendurelab.github.io/LACHESIS/

ReMILO: reference assisted misassembly detection algorithm using short and long reads.

Jit — Fri, 06 Jul 2018 04:27:49 -0500

ReMILO, a reference assisted misassembly detection algorithm that uses both short reads and PacBio SMRT long reads. ReMILO aligns the initial short reads to both the contigs and reference genome, and then constructs a novel data structure called red-black multipositional de Bruijn graph to detect misassemblies. In addition, ReMILO also aligns the contigs to long reads and find their differences from the long reads to detect more misassemblies.

Address of the bookmark: https://github.com/songc001/remilo

LRCstats: a tool for evaluating long reads correction methods

Aaryan Lokwani — Wed, 22 Aug 2018 11:05:04 -0500

LRCstats is an open-source pipeline for benchmarking DNA long read correction algorithms for long reads outputted by third generation sequencing technology such as machines produced by Pacific Biosciences. The reads produced by third generation sequencing technology, as the name suggests, are longer in length than reads produced by next generation sequencing technologies, such as those produced by Illumina. However, long reads are plagued by high error rates, which can cause issues in downstream analysis. Long read correction algorithms reduce the error rate of long reads either through self-correcting methods or using accurate, short reads outputted by next generation sequencing technologies to correct long reads.

Address of the bookmark: https://github.com/cchauve/lrcstats

BASE: a practical de novo assembler for large genomes using long NGS reads

Rahul Nayak — Fri, 19 Oct 2018 07:25:21 -0500

new de novo assembler called BASE. It enhances the classic seed-extension approach by indexing the reads efficiently to generate adaptive seeds that have high probability to appear uniquely in the genome. Such seeds form the basis for BASE to build extension trees and then to use reverse validation to remove the branches based on read coverage and paired-end information, resulting in high-quality consensus sequences of reads sharing the seeds. Such consensus sequences are then extended to contigs.

Address of the bookmark: https://github.com/dhlbh/BASE