• A compiled program delivering high performance analyses
• Supports FASTA/FASTQ files, also Gzip compressed
• A growing collection of handy utilities, also for quick inspection of the datasets

Can be easily installed via conda:

conda install -c bioconda seqfu

Address of the bookmark: https://telatin.github.io/seqfu2/

Tutorial https://github.com/andyrimmer/Platypus/blob/master/misc/README.txt

Address of the bookmark: http://www.well.ox.ac.uk/platypus

More at https://kevlar.readthedocs.io/en/latest/

https://www.cell.com/iscience/pdf/S2589-0042(19)30259-7.pdf

Address of the bookmark: https://github.com/kevlar-dev/kevlar

Given benchmark and comparsion sets of SVs, calculate the recall, precision, and f-measure.

Spiral Genetics

Motivation

Address of the bookmark: https://github.com/spiralgenetics/truvari

For detail : http://www.sciencemag.org/content/341/6143/281

http://www.npr.org/blogs/health/2013/07/18/203298244/worlds-biggest-virus-may-have-ancient-roots

The ongoing 2014 West Africa Ebola outbreak is considered to be the largest and longest outbreak ever recorded of Ebola, killing at least 932 people and infecting more than 1,700 till date since March in Sierra Leone, Guinea, Nigeria and Liberia.

Hence, the World Health Organisation (WHO) on 8 August, 2014 declared the killer Ebola epidemic ravaging parts of West Africa an international health emergency.

Causes

EVD is caused by infection with a virus of the family Filoviridae, genus Ebolavirus. While there are five identified sub-species of Ebolavirus, four viruses cause disease in humans. They are Bundibugyo virus (BDBV), Ebola virus (EBOV), Sudan virus (SUDV), Taï Forest virus (TAFV).

The fifth virus, Reston virus (RESTV), is not considered to be disease-causing in humans.

According to WHO, EVD first appeared in 1976 in two simultaneous outbreaks, in Nzara, Sudan, and in Yambuku, Democratic Republic of Congo. The latter was in a village situated near the Ebola River from which the disease takes its name.

How does it spread?

It is still unclear how Ebola spreads. However, it is believed that the first pateint becomes infected through contact with an infected animal's body fluids.

Human-to-human transmission can occur through direct contact with blood, organs or other body fluids of infected people or exposure to objects such as needles and syringes that have been contaminated with infected secretions.

Ebola can also be transmitted from men who have recovered from the disease through semen as it is infectious for up to 7 weeks.

Infected dead bodies can spread Ebola as they are still infectious. So mourners who have direct contact with the body of deceased person can also get the disease.

Who is most at risk?

Health-care workers who do not wear appropriate protective clothing and family members who are in close contact with infected people or deceased patients.

Signs and symptoms:

Symptoms may occur between 2 and 21 days after contracting the infection. Common signs of Ebola include:

Fever

Headache

Muscle, abdominal and joint pain

Sore throat

Weakness

Diarrhea

Vomit or cough up blood

Chest pain

Difficulty in breathing and swallowing

Rash

Hiccups

Bleeding inside and outside the body

Prevention

Currently there is no vaccine available for humans. But the infection can be controlled through the use of recommended protective measures such as:

Avoid contacting infected blood or secretions, including from those who are dead .

Using standard precautions for all patients in the healthcare setting.

Sterilizing equipment, and wearing protective clothing including masks, gloves, gowns and goggles.

Washing your hands with soaps or detergents.

Disinfecting your surroundings.

Isolate people who have Ebola symptoms.

Culling of infected animals, with close supervision of burial or incineration of carcasses.

Yet, not travelling to the areas or countries where the virus is found is the best way to avoid Ebola.

Zoonotic Henipavirus

https://pubmed.ncbi.nlm.nih.gov/35921459/

https://www.ncbi.nlm.nih.gov/nuccore/OM069646,,OM069567,OM069568,OM069569,OM069570,OM069571,OM069572,OM069573,OM069574,OM069575,OM069576,OM069577,OM069578,OM069579,OM069580,OM069581,OM069582,OM069583,OM069584,OM069585,OM069586,OM069587,OM069588,OM069589,OM069590,OM069591,OM069592,OM069593,OM069594,OM069595,OM069596,OM069597,OM069598,OM069599,OM069600,OM069601,OM069602,OM069603,OM069604,OM069605,OM069606,OM069607,OM069608,OM069609,OM069610,OM069611,OM069612,OM069613,OM069614,OM069615,OM069616,OM069617,OM069618,OM069619,OM069620,OM069621,OM069622,OM069623,OM069624,OM069625,OM069626,OM069627,OM069628,OM069629,OM069630,OM069631,OM069632,OM069633,OM069634,OM069635,OM069636,OM069637,OM069638,OM069639,OM069640,OM069641,OM069642,OM069643,OM069644,OM069645,OM069646

Source: Life technologies

Address of the bookmark: http://www.lifetechnologies.com/global/en/home/communities-social/blog/blogs/sequencing-solutions-to-world-health.html?cid=social_blogseries_20130829_11098264

Adapter sequences:
Optimal enzymes for amplifying sequencing libraries.
Quail, M. a et al. Nat. Methods 9, 10-1 (2012).

GAGE:
GAGE: A critical evaluation of genome assemblies and assembly algorithms.
Salzberg, S. L. et al. Genome Res. 22, 557-67 (2012).

KMC:
Disk-based k-mer counting on a PC.
Deorowicz, S., Debudaj-Grabysz, A. & Grabowski, S. BMC Bioinformatics 14, 160 (2013).

Kraken:
Kraken: ultrafast metagenomic sequence classification using exact alignments.
Wood, D. E. & Salzberg, S. L. Genome Biol. 15, R46 (2014).

MUMmer:
Versatile and open software for comparing large genomes.
Kurtz, S. et al. Genome Biol. 5, R12 (2004).

R:
R: A language and environment for statistical computing.
R Core Team (2013). R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org/.

RATT:
RATT: Rapid Annotation Transfer Tool.
Otto, T. D., Dillon, G. P., Degrave, W. S. & Berriman, M. Nucleic Acids Res. 39, e57 (2011).

SAMtools:
The Sequence Alignment/Map format and SAMtools.
Li, H. et al. Bioinformatics 25, 2078-9 (2009).

Trimmomatic:
Trimmomatic: A flexible trimmer for Illumina Sequence Data.
Bolger, A. M., Lohse, M. & Usadel, B. Bioinformatics 1-7 (2014).

• BigDataScript – A cross-system scripting language for working with big data pipelines in computer systems of different sizes and capabilities. [ paper-2014 | web ]
• Bpipe – A small language for defining pipeline stages and linking them together to make pipelines. [ web ]
• Common Workflow Language – a specification for describing analysis workflows and tools that are portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing (HPC) environments. [ web ]
• Cromwell – A Workflow Management System geared towards scientific workflows. [ web ]
• Galaxy – a popular open-source, web-based platform for data intensive biomedical research. Has several features, from data analysis to workflow management to visualization tools. [ paper-2018 | web ]
• Nextflow (recommended) – A fluent DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner. [ paper-2018 | web ]
• Ruffus – Computation Pipeline library for python widely used in science and bioinformatics. [ paper-2010 | web ]
• SeqWare – Hadoop Oozie-based workflow system focused on genomics data analysis in cloud environments. [ paper-2010 | web ]
• Snakemake – A workflow management system in Python that aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment. [ paper-2018 | web ]
• Workflow Descriptor Language – Workflow standard developed by the Broad. [ web ]