BOL: Related items

ALLHiC: Phasing and scaffolding polyploid genomes based on Hi-C data

BioStar — Thu, 20 Dec 2018 12:03:32 -0600

The major problem of scaffolding polyploid genome is that Hi-C signals are frequently detected between allelic haplotypes and any existing stat of art Hi-C scaffolding program links the allelic haplotypes together. To solve the problem, we developed a new Hi-C scaffolding pipeline, called ALLHIC, specifically tailored to the polyploid genomes. ALLHIC pipeline contains a total of 5 steps: prune, partition, rescue, optimize and build.

Address of the bookmark: https://github.com/tangerzhang/ALLHiC/wiki

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

NextDenovo: string graph-based de novo assembler for TGS long reads

Jit — Sun, 05 Jan 2020 04:08:29 -0600

NextDenovo is a string graph-based de novo assembler for TGS long reads. It uses a "correct-then-assemble" strategy similar to canu, but requires significantly less computing resources and storages. After assembly, the per-base error rate is about 97-98%, to further improve single base accuracy, please use NextPolish.

NextDenovo contains two core modules: NextCorrect and NextGraph. NextCorrect can be used to correct TGS long reads with approximately 15% sequencing errors, and NextGraph can be used to construct a string graph with corrected reads. It also contains a modified version of minimap2 for adapting input and output and producing more sensitive and accurate dovetail overlaps, and some useful utilities (see here for more details).

Address of the bookmark: https://github.com/Nextomics/NextDenovo

HASLR: a hybrid assembler which uses both second and third generation sequencing reads

BioStar — Mon, 04 May 2020 02:04:03 -0500

HASLR, a hybrid assembler which uses both second and third generation sequencing reads to efficiently generate accurate genome assemblies. Our experiments show that HASLR is not only the fastest assembler but also the one with the lowest number of misassemblies on all the samples compared to other tested assemblers. Furthermore, the generated assemblies in terms of contiguity and accuracy are on par with the other tools on most of the samples. Availability. HASLR is an open source tool available at https://github.com/vpc-ccg/haslr.

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

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/

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

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/

BamView: a free interactive display of read alignments in BAM data files

Neel — Fri, 09 Nov 2018 13:43:22 -0600

To run the application on UNIX from the downloaded jar file run the UNIX:

java -mx512m -jar BamView.jar

and extra command line options are given when '-h' is used:

java -jar BamView.jar -h

BAM files can be specified on the command line with the '-a' option:

java -mx512m -jar BamView.jar -a pathToFile/sorted.bam

If a BAM filename is not given on the command line BamView will prompt for a file to be entered. The BAM index file should have the same name as the BAM file but with a '.bai' suffix. Multiple BAM files can be loaded and overlaid in the viewer. To make this easier BamView will read in files that contain a list of filenames.

Address of the bookmark: http://bamview.sourceforge.net/

EAGLER: a scaffolding tool for long reads.

Jit — Mon, 04 Jun 2018 05:26:03 -0500

EAGLER is a scaffolding tool for long reads. The scaffolder takes as input a draft genome created by any NGS assembler and a set of long reads. The long reads are used to extend the contigs present in the NGS draft and possibly join overlapping contigs. EAGLER supports both PacBio and Oxford Nanopore reads.

The tool should be compatible with most UNIX flavors and has been successfully tested on the following operating systems:

Mac OS X 10.11.1
Mac OS X 10.10.3
Ubuntu 14.04 LTS

https://bib.irb.hr/datoteka/844447.Diplomski_2015_Luka_terbi.pdf

Address of the bookmark: https://github.com/mculinovic/EAGLER