How to find a better performance NIPT analysis scripts ?
1
0
Entering edit mode
8.6 years ago
winter_li ▴ 60

HI, I wanna find a NIPT pipeline ,but I do not which is better pipeline ? So can you recommend a complete pipeline scripts ?

thank you !!!

genome R gene next-gen sequencing • 3.0k views
ADD COMMENT
0
Entering edit mode

For what data source? Array? NGS? In what language? For what disorders?

ADD REPLY
0
Entering edit mode

HI, data source is WGS data of next generation sequencing . R and Perl ,or python , better perl . T21,T13 and T18.

Thank you !

ADD REPLY
0
Entering edit mode
8.6 years ago
Roy • 0

I'm the author of this set of scripts: https://github.com/rstraver/wisecondor

It seems rather popular and is used in several medical centres across the world for diagnostics on calling T13 T18 and T21. Feel free to ask questions on my work if you need help.

As for other works, I think RAPIDR is the most recent package I heard of in papers. I don't have a full list ready of alternative packages but most comparisons I've seen lately are between this and my work.

ADD COMMENT
0
Entering edit mode

The OP has gone on to use RAPIDR according to more recent posts asking for further help, so an alternative may be welcome for them!

ADD REPLY
0
Entering edit mode

HI , OP ? what's the full name of OP ?

ADD REPLY
0
Entering edit mode

OP is shorthand for Original Poster, which is you in this specific case, winter_li ;)

I also realised you went with RAPIDR from your posts (as Daniel Swan noted), after I submitted my response.

I see you asked a few more things now, but I'm not exactly hanging around on biostars on a daily basis, sorry for that. Happy to learn you found you could also ask through GitHub!

ADD REPLY
0
Entering edit mode

thank you ,Roy, I will have a try .

ADD REPLY
0
Entering edit mode

HI , I need to cut adapter sequence from single-end fastq of NIPT ? which tool should use ?

ADD REPLY
1
Entering edit mode

123Fastq has 2 approaches for trimming adapter contaminations. also have graphical user interface. https://sourceforge.net/projects/project-123ngs/

ADD REPLY

Login before adding your answer.

Traffic: 2605 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6