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Aplicacións

fastqsim

Versións dispoñibles:

FinisTerraeII

  • 3.0

Descrición


The software provides two types of capabilities: 
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1. Next Generation Sequencing (NGS) datasets characterization. Characterization refers to the following: 
   a. Histogram of read length.
   b. Min/Max/Mean quality scores for each base position in a read. 
   c. Insertion characterization. This refers to calculating the probability of an insertion at each position in a sequence, the probability of insertions of a particular size, and the probability of a repeat insertion of a particular size. 
   d. Deletion characterization, same parameters as insertions. 
   e. Single base pair mutations. This refers to calculating the probability of a mutation at each position in a sequence, the probability of mutating from one base to another       (i.e. c--> g versus c--> a) 
   f. Primer histogram. By computing the frequency of each primer, "pileups" of low complexity reads can be detected. 
   g. Read alignment quality histogram. Read alignment refers to the percent of a read from the data that aligns to a matching hit from the BLAST database. This value depends on the data quality and the instrument used: the value is around 98% for Roche 454 data, but around 90% for PacBio data.   
2. "Spiking" of reads from a fasta source into a background fastq dataset. The spiking is performed in a manner such that the characteristics of the spiked reads are identical    to those of the background reads, so a spiked read is indistinguishable from a background read. 

Guía de uso


Please use the following module commands:

module av fastqsim

Check the fastqsim available versions

module help fastqsim

Get a brief server specific user guide

module load fastqsim

Load default version environment

module load fastqsim/<version>

Load specific version environment

URL Manual

Soporte


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