BCL2FASTQ WEB UI Pipeline , Web Services (Mono C#), Shell Scripts, Linux HPC, Illumina HISEQ 2500 Sequencing on our lab :D

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I’m still using Mono on Bioinformatics !!

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La orden de ejecución del Pipeline se lleva a cabo a través de un servicio web que se consume a través de una interfaz gráfica de usuario simple, la cual es desarrollada bajo Google Web Kit.

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El Servicio Web está desarrollado en C# en Linux totalmente y corre bajo el Application Server Mono XSP4 usando un profile de .NET Framework 4 bajo un sistema operativo empresarial CentOS Linux como lo es en nuestro caso el nodo maestro de nuestro Cluster de Computo HPC de operación principal.

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No hace falta mencionar que la aplicación web que se ha desarrollado usa sin duda herramientas como DojoToolkit, JQuery y varias librerías excelentes =D

La siguiente imagen solo muestra un extracto de las operaciones que el Pipeline va ejecutando durante su flujo de operación:

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Fixed Gap2Caf Tools for MIRA 4.x Genome Assembly

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In past days I was trying to assemble , using denovo method of course, mapped SOLiD reads using MIRA assembler and the results were successful. The mira assembler generate full assemblie formats like caf or maf and other formats like fasta, quality value, wig and tcs files, I´m sure that you will need to convert formats to reach some tools like assembly viewers, editors or scaffolders.

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How to install PoreTools a toolkit for working with nanopore sequencing data Fast5 from Oxford Nanopore in CentOS Linux 6

Introduction

Poretools is a flexible toolkit for manipulating and exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.
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Poretools operates directly on the native FAST5 (a variant of the HDF5 standard) file format produced by ONT and provides a wealth of format conversion utilities and data exploration and visualization tools.

I will to tell you how to install this awesome python command line application in CentOS Linux 6.x

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Labsergen BCL2FASTQ Pipeline

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The BCL2FASTQ Pipeline consists of an interface in command line, flexible and friendly, which I developed in the LANGEBIO Genomic Services department because we need to make use of illumina’s software applications in a more simple way.

The BCL2FASTQ Pipeline allows to :

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LabSerGen Genotyping By Sequencing Pipeline version 0.2

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El año pasado desarrollamos en el Laboratorio de Servicios Genómicos del Langebio Cinvestav un Pipeline para trabajar con GBS (Genotyping By Sequencing) principalmente para los datos generados por el resultado del proceso de Secuenciación en las plataformas Illumina HiSeq and MiSeq.

El Pipeline ejecuta las siguientes tareas:

  1. Filtrado de Reads
  2. Indexado,si es que es necesario, de Genoma de Referencia para el Alineamiento de Reads.
  3. Alineamiento de Reads
  4. …..

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App: Illumina UMSi for HISEQ and MiSEQ

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I developed this based desktop app using Visual Basic 6 programming language for the illumina instrument HiSeq and MiSeq.

This desktop app runs on Microsoft Windows 7 it allows to attach a Linux Network Storage via smb protocol . software requirements are Linux distribution running Samba daemon and the shares properly set.

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How to Uninstall Roche 454 Data Analysis, Data Processing v2.8 @ CentOS Linux 5.x ?

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I’m trying uninstall via rpm package managment and works for me :),
following my instructions you could downgrade software versions :)

you will need to list all roche 454 software installed via rpm (main setup.sh )

[jacob]$ rpm -q –all | grep gs

gsMapper-2.8-1
gsNewbler-2.8-1
gsRunProcessor-2.8-1
gsRunProcessorManager-2.6-1
gsSeqTools-2.8-1
gsAmplicons-2.8-1

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VCF Lib – for parsing and manipulating VCF files FIXED

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like Erik said in his github vcf lib project:

The Variant Call Format (VCF) is a flat-file, tab-delimited textual format intended to concisely describe reference-indexed variations between individuals. The current specification can be found on the 1000 Genomes wiki (http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41)

VCFLib is a simple C++ library for parsing and manipulating VCF files, + many command-line utilities

In pasts weeks I was trying to install VCFLib our HPC Cluster Computer but I had some problems to compile it , I fixed it , follow instructions below

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SOLiD2FASTQ ¿Cómo convertir ColorSpace/Qual a FASTQ?

Un problema al que te enfrentas muy seguido es como generar un archivo FASTQ a partir de tus secuencias en colores (*.csfasta) y valores de calidad (*.qual) resultado de la secuenciación por ligación de la serie de instrumentos SOLiD de la conocida empresa LifeTechnologies/AB. Vamos directo al grano sin hacer mucho alarde , de igual…

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Velvet Sequence assembler for very short reads + OpenMP

OpenMP allows a program to make use of multiple CPU cores on the same machine. I will try to use Velvet Assembler with OpenMP support. Step 1. Check if you have OpenMP enabled in your computer. Copy following C source code #include <omp.h> #include <stdio.h> int main() { #pragma omp parallel printf(“Hello from thread %d,…

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unofficial patch XSQ Tools/Linux Mint 12 Lisa

Hi guys , I’m still alive .. I developed simple patch for Life Technologies/Applied Biosystems XSQ Tools. This patch allows to run XSQ Tools in Debian based linux distributions like Linux Mint 12 or Ubuntu Linux 1. Download XSQ Tools from official website. 2. Decompress tar file $ tar -zxvf XSQ_Tools_20120109.tgz 3. Download patch tar…

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EBI Wise 2 plus updated SQUID available.

The Wise2 package is entirely open source licensed for use by both commerical and academic sites. This means that anyone can modify and
redistribute the source code without restriction. However, the use of the source code as part of a larger, and potentially propietary package depends on which portions of the source code you wish to use. Each directory has a seperate LICENSE or GNULICENSE file which you
should read, but the gist is given below.

Download updated EBI Wise 2 from here

Download from EBI (outdated version)

Installation instructions here or INSTALL

Currently I’m packaging (deb and rpm) EBI Wise 2 binaries for Debian and Red Hat based linux distros.

Jacob

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