BOL: Related items

MITOS: improved de novo metazoan mitochondrial genome annotation

Jit — Fri, 26 Oct 2018 08:25:39 -0500

Allows automatic annotation of metazoan mitochondrial genomes. MITOS is a pipeline designed to compute a consistent de novo annotation of the mitogenomic sequences. The software allows for a systematic error screening, the standardisation of gene name and gene boundary designation, anticodon labelling of tRNAs, and provides the means for the assessment of the validity of a gene assignment.

Address of the bookmark: http://mitos.bioinf.uni-leipzig.de/index.py

ASCIIGenome: genome browser based on command line interface and designed for running from console terminals.

Neel — Fri, 09 Nov 2018 13:50:04 -0600

ASCIIGenome is a genome browser based on command line interface and designed for running from console terminals.

Since ASCIIGenome does not require a graphical interface it is particularly useful for quickly visualizing genomic data on remote servers while offering flexibility similar to popular GUI viewers like IGV.

Documentation is at readthedocs/asciigenome.

Address of the bookmark: https://github.com/dariober/ASCIIGenome

Genobuntu: A software package containing more than 70 software and packages oriented towards NGS and genome assembly

BioStar — Tue, 11 Dec 2018 05:15:57 -0600

Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools.

Commonly used biological software and example script files for different assembly pipelines have also been provided, where the example script files can be updated to suit one’s experimental needs. Genobuntu attempts to reduce the amount of time and energy needed to build software workstations and it can also act as a good teaching source for a class room setting.

https://sourceforge.net/projects/genobuntu/

Address of the bookmark: https://sourceforge.net/projects/genobuntu/

Versatile genome assembly evaluation with QUAST-LG

Jit — Fri, 21 Dec 2018 22:06:31 -0600

QUAST-LG is an extension of QUAST intended for evaluating large-scale genome assemblies (up to mammalian-size).

QUAST-LG is included in the QUAST package starting from version 5.0.0 (download the latest release). Run QUAST as usual and do not forget to add ‐‐large option to your command!

A short list of the new features (see CHANGES for all):

Significant speedup achieved by both use of new fast aligner (minimap2) and the refactoring of alignment analyzing modules
New k-mer-based completeness and correctness metrics
BUSCO added for enhanced reference-free analysis
The concept of upper bound assembly (theoretical limits on the assembly completeness and contiguity for a given genome and set of reads)

Address of the bookmark: http://cab.spbu.ru/software/quast-lg/

LTR_Finder: an efficient program for finding full-length LTR retrotranspsons in genome sequences.

Neel — Sun, 13 Jan 2019 07:05:53 -0600

LTR_Finder is an efficient program for finding full-length LTR retrotranspsons in genome sequences.

The Program first constructs all exact match pairs by a suffix-array based algorithm and extends them to long highly similar pairs. Then Smith-Waterman algorithm is used to adjust the ends of LTR pair candidates to get alignment boundaries. These boundaries are subject to re-adjustment using supporting information of TG..CA box and TSRs and reliable LTRs are selected. Next, LTR_FINDER tries to identify PBS, PPT and RT inside LTR pairs by build-in aligning and counting modules. RT identification includes a dynamic programming to process frame shift. For other protein domains, LTR_FINDER calls ps_scan (from PROSITE, http://www.expasy.org/prosite/) to locate cores of important enzymes if they occur.

Address of the bookmark: https://github.com/xzhub/LTR_Finder

CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS variants

BioJoker — Tue, 09 Apr 2019 07:23:37 -0500

Validated a widely accessible approach that can be used to establish functional causality for noncoding sequence variants identified by GWASs.

https://www.nature.com/articles/nm.3975

Address of the bookmark: https://www.nature.com/articles/nm.3975

5700 year-old human genome !

Jit — Thu, 19 Dec 2019 11:22:18 -0600

A Landmark in genomics, scientists have done something that hasn't been done ever.

Scientists have reconstructed the genome of an ancient human who lived nearly 5,700 years ago in Southern Denmark from the birch pitch- an ancient tar-like substance.

By sequencing the sample, researchers not only discovered the ancient human DNA but also microbial DNA reflecting the oral microbiome of the person who chewed the pitch, along with plant and animal DNA that could be the recent meal she might have consumed.

The DNA sample is comparable in quality to well-preserved teeth and skull bones. The DNA suggests that the chewer was a female, most likely with dark skin, dark brown hair and blue eyes.

https://www.nature.com/articles/s41467-019-13549-9

Artistic reconstruction. (Tom Björklund)

More at https://gizmodo.com/scientists-reconstruct-lola-after-finding-her-dna-in-1840481633

mutatrix: a population genome simulator which generates simulated genomes.

Jit — Tue, 28 Jan 2020 04:06:58 -0600

genome simulation across a population with zeta-distributed allele frequency, snps, insertions, deletions, and multi-nucleotide polymorphisms

More at https://github.com/ekg/mutatrix

./mutatrix -S sample -P test/ -p 2 -n 10 reference.fasta

Address of the bookmark: https://github.com/ekg/mutatrix

China’s BGI says it can sequence a genome for just $100

Neel — Sat, 29 Feb 2020 04:49:43 -0600

Using technology originally acquired in the US, the Chinese gene giant BGI Group says it will make genome sequencing cheaper than ever, breaking the $100 barrier for the first time.

The Shenzhen company says the low cost will be possible with an “extreme” DNA sequencing system it plans to offer that is capable of decoding the genomes of 100,000 people a year.

Ref: https://www.technologyreview.com/s/615289/china-bgi-100-dollar-genome/

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