SEQanswers

Go Back   SEQanswers > Literature Watch



Similar Threads
Thread Thread Starter Forum Replies Last Post
PubMed: Inference of Site Frequency Spectra From High-throughput Sequence Data: Quant Newsbot! Literature Watch 0 05-22-2011 06:23 AM
PubMed: Accurate and exact CNV identification from targeted high-throughput sequence Newsbot! Literature Watch 0 04-15-2011 12:30 AM
PubMed: GeneScreen: a program for high-throughput mutation detection in DNA sequence Newsbot! Literature Watch 0 11-03-2010 11:20 AM
PubMed: High resolution transcriptome maps for wild-type and NMD mutant C. elegans th Newsbot! Literature Watch 0 09-26-2009 03:04 AM
PubMed: High-throughput sequence-based epigenomic analysis of Alu repeats in human ce Newsbot! Literature Watch 0 05-22-2009 06:00 AM

Reply
 
Thread Tools
Old 01-22-2010, 03:10 AM   #1
Newsbot!
RSS Posting Maniac
 

Join Date: Feb 2008
Posts: 1,443
Default PubMed: SeqTrim: a high-throughput pipeline for preprocessing any type of sequence re

Syndicated from PubMed RSS Feeds

Related Articles SeqTrim: a high-throughput pipeline for preprocessing any type of sequence reads.

BMC Bioinformatics. 2010 Jan 20;11(1):38

Authors: Falgueras J, Lara AJ, Fernandez-Pozo N, Canton FR, Perez-Trabado G, Claros MG

ABSTRACT: BACKGROUND: High-throughput automated sequencing has enabled an exponential growth rate of sequencing data. This requires increasing sequence quality and reliability in order to avoid database contamination with artefactual sequences. The arrival of pyrosequencing enhances this problem and necessitates customisable pre-processing algorithms. RESULTS: SeqTrim has been implemented both as a Web and as a standalone command line application. Already-published and newly-designed algorithms have been included to identify sequence inserts, to remove low quality, vector, adaptor, low complexity and contaminant sequences, and to detect chimeric reads. The availability of several input and output formats allows its inclusion in sequence processing workflows. Due to its specific algorithms, SeqTrim outperforms other pre-processors implemented as Web services or standalone applications. It performs equally well with sequences from EST libraries, SSH libraries, genomic DNA libraries and pyrosequencing reads and does not lead to over-trimming. CONCLUSIONS: SeqTrim is an efficient pipeline designed for pre-processing of any type of sequence read, including next-generation sequencing. It is easily configurable and provides a friendly interface that allows users to know what happened with sequences at every pre-processing stage, and to verify pre-processing of an individual sequence if desired. The recommended pipeline reveals more information about each sequence than previously described pre-processors and can discard more sequencing or experimental artefacts.

PMID: 20089148 [PubMed - as supplied by publisher]



More...
Newsbot! is offline   Reply With Quote
Old 08-02-2010, 12:48 AM   #2
lvxiaobao
Junior Member
 
Location: guangzhou city ,guangdong province ,china

Join Date: Oct 2009
Posts: 6
Default

thanks, i'll have a try
lvxiaobao is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 08:41 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO