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

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

LoRMA: a tool for correcting sequencing errors in long reads such those produced by Pacific Biosciences sequencing machines

Jit — Wed, 15 Jun 2016 17:18:36 -0500

LoRMA is a tool for correcting sequencing errors in long reads such those produced by Pacific Biosciences sequencing machines.

Publication:

L. Salmela, R. Walve, E. Rivals, and E. Ukkonen: Accurate selfcorrection of errors in long reads using de Bruijn graphs. Accepted to RECOMB-Seq 2016.

Download:

Address of the bookmark: https://www.cs.helsinki.fi/u/lmsalmel/LoRMA/

lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data

BioJoker — Tue, 27 Nov 2018 04:43:57 -0600

lordFAST is a sensitive tool for mapping long reads with high error rates. lordFAST is specially designed for aligning reads from PacBio sequencing technology but provides the user the ability to change alignment parameters depending on the reads and application.

lordFAST, a novel long-read mapper that is specifically designed to align reads generated by PacBio and potentially other SMS technologies to a reference. lordFAST not only has higher sensitivity than the available alternatives, it is also among the fastest and has a very low memory footprint.

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

Indexcov: fast coverage quality control for whole-genome sequencing

Jit — Wed, 29 Aug 2018 09:20:46 -0500

indexcov, an efficient estimator of whole-genome sequencing coverage to rapidly identify samples with aberrant coverage profiles, reveal large-scale chromosomal anomalies, recognize potential batch effects, and infer the sex of a sample. Indexcov is available at https://github.com/brentp/goleft under the MIT license.

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

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

DeepVariant : an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Jit — Sat, 25 Jan 2020 13:28:09 -0600

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. DeepVariant relies on Nucleus, a library of Python and C++ code for reading and writing data in common genomics file formats (like SAM and VCF) designed for painless integration with the TensorFlow machine learning framework.

https://ai.googleblog.com/2017/12/deepvariant-highly-accurate-genomes.html

https://www.biorxiv.org/content/10.1101/092890v6

Address of the bookmark: https://github.com/google/deepvariant

MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads

Rahul Nayak — Fri, 11 May 2018 05:07:45 -0500

MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads. MECAT employs novel alignment and error correction algorithms that are much more efficient than the state of art of aligners and error correction tools. MECAT can be used for effectively de novo assemblying large genomes. For example, on a 32-thread computer with 2.0 GHz CPU , MECAT takes 9.5 days to assemble a human genome based on 54x SMRT data, which is 40 times faster than the current PBcR-Mhap pipeline. MECAT performance were compared with PBcR-Mhap pipeline, FALCON and Canu(v1.3) in five real datasets. The quality of assembled contigs produced by MECAT is the same or better than that of the PBcR-Mhap pipeline and FALCON.

https://www.nature.com/articles/nmeth.4432

Address of the bookmark: https://github.com/xiaochuanle/MECAT

npScarf: real-time scaffolder using SPAdes contigs and Nanopore sequencing reads

Shruti Paniwala — Mon, 11 Jun 2018 05:14:57 -0500

npScarf (jsa.np.npscarf) is a program that connect contigs from a draft genomes to generate sequences that are closer to finish. These pipelines can run on a single laptop for microbial datasets. In real-time mode, it can be integrated with simple structural analyses such as gene ordering, plasmid forming.

Address of the bookmark: http://japsa.readthedocs.io/en/latest/tools/jsa.np.npscarf.html

CoLoRMap: Correcting Long Reads by Mapping short reads

Jit — Mon, 20 Aug 2018 14:17:05 -0500

Second generation sequencing technologies paved the way to an exceptional increase in the number of sequenced genomes, both prokaryotic and eukaryotic. However, short reads are difficult to assemble and often lead to highly fragmented assemblies. The recent developments in long reads sequencing methods offer a promising way to address this issue. However, so far long reads are characterized by a high error rate, and assembling from long reads require a high depth of coverage. This motivates the development of hybrid approaches that leverage the high quality of short reads to correct errors in long reads.We introduce CoLoRMap, a hybrid method for correcting noisy long reads, such as the ones produced by PacBio sequencing technology, using high-quality Illumina paired-end reads mapped onto the long reads. Our algorithm is based on two novel ideas: using a classical shortest path algorithm to find a sequence of overlapping short reads that minimizes the edit score to a long read and extending corrected regions by local assembly of unmapped mates of mapped short reads. Our results on bacterial, fungal and insect data sets show that CoLoRMap compares well with existing hybrid correction methods.The source code of CoLoRMap is freely available for non-commercial use at https://github.com/sfu-compbio/colormap

ehaghshe@sfu.ca or cedric.chauve@sfu.ca

Address of the bookmark: https://github.com/sfu-compbio/colormap