Thursday, 15 July 2021

Running Kraken2 and creating a Krona report

 Had to work with Ion Torrent BAMs for this but I think it's applicable to everything

  Needed to run this on unmapped reads so running this first.

After that the next script is fairly simple 

Will share the install when I have time. A major hiccup for me was realising not all pre-built db works with Kraken2

Thursday, 13 May 2021

This command allows you to see what apps are consuming internet. ss -p

 

This command allows you to see what apps are consuming internet.

ss -p

Monday, 15 March 2021

GenomSys Banks on MPEG-G Standard to Make Genome Analysis Mobile

 This software company did something that I didn't expect... putting the variant calling on the phone itself ..

"The variant calling is run directly on the phone, extracting the data from the file on your phone, processed on the phone, and only at the end the VCF file could be shared in the cloud for annotation and reporting by an accredited physician," Ascari said. The physician is necessary to assure that the result is of "diagnostic quality," he added.

I honestly expected CRAM & cloud based calling with encrypted exchange (made feasible with 5G mobile network) of bam reads with an app store like customised reports for what you want to know about your genetics. 

Other than security concerns, I don't see why I would want variant calling on the phone though.

Previous posts

IonCRAM: a reference-based compression tool for ion torrent sequence files 

Future of Genomics: 10 bold predictions

What 5G mobile networks portends for the future of personal genomics

 

 

 

Thursday, 12 November 2020

A novel BRCA2 splice variant identified in a young woman

 Sharing a newly published article where a novel c.682‐2delA variant involving the AG consensus at the 3′ end of BRCA2 intron 8 was detected. The case involved a 33‐year‐old Italian breast cancer patient belonging to a HBOC family (BRCAPro score: 88%) with no other known pathogenic BRCA mutation. 

 

A novel BRCA2 splice variant identified in a young woman - Nicolussi - - Molecular Genetics & Genomic Medicine

Wednesday, 4 November 2020

de novo assembly of Ion Torrent Reads

 I am intrigued that this Genome assembly guide includes mention of SOLID and Ion Torrent ... although not much information is given on how to work on them for genome assembly. 

That said, perhaps the SPADES plugin provided with the sequencer solves most of everyone's immediate needs ... Wondering how improve on evaluating the assemblies 



Thursday, 29 October 2020

IonCRAM: a reference-based compression tool for ion torrent sequence files

 IonCRAM: a reference-based compression tool for ion torrent sequence files https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7487613/ 

 IonCRAM, the first reference-based compression tool to compress Ion Torrent BAM files for long term archiving. For the BAM files, IonCRAM could achieve a space saving of about 43%. This space saving is superior to what achieved with the CRAM format by about 8–9%.

Future research for reducing the space consumption of the Ion Torrent BAM files would include the binning of the flow signal and quality values. The idea of binning was initially introduced by Illumina [] to reduce the space consumption of the quality values. This initiative was immediately followed by intensive research to optimize the binning procedure and address its effect on the downstream analysis, especially on the variant calling step []. We think that the binning of flow signals and quality data of Ion Torrent would also be successful, provided that the manufacturer contribute to this research. We added an option to IonCRAM for binning the flow signals, in a similar way to the binning method implemented in [], and measured its effect on compression (Supplementary File 1). We left the step for investigating the effect of this binning on the downstream analysis to further research.

It is worth mentioning that IonCRAM has not been only used for the test data in the paper, it has also been used to compress and backup thousands of files for the Saudi Human Genome Program. IonCRAM is an open source and it is available for free along with the related test data at the tool website http://ioncram.saudigenomeproject.com.

  

Static ip on Jessie Raspbian with dhcpcd.conf


Static IP address templates for dhcpcd.conf

https://www.raspberrypi.org/forums/viewtopic.php?t=140252

######################################################
# TEMPLATE: A static IP address only when no DHCP
#
#           The profile name is arbitrary. Use "fred"
#           if you want. Not much we can put as
#           default servers, but set them up as
#           you usually would.
######################################################
interface eth0
fallback nodhcp

profile nodhcp
static ip_address=10.0.0.1/8
static routers=10.0.0.1
static domain_name_servers=10.0.0.1


Trying to do this

https://www.diyhobi.com/share-raspberry-pi-wifi-internet-ethernet/

Datanami, Woe be me