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


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.

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


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


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


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 ?


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 )

[jacob]$ rpm -q –all | grep gs


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VCF Lib – for parsing and manipulating VCF files FIXED


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 (

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.


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[Fixed] EBI Wise 2 runs on Linux Mint 12 Lisa

I fixed SQUID C library for EBI Wise2 bioinformatics software application.

Wise 2 was developed in C by Ewan Birney. EBI Wise 2 software compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors.

I will explain step by step how to fix SQUID and install Wise 2 in your current Linux Mint “Lisa” OS (aka Ubuntu)

$ mv sqio.c sqio.c.bk

3. try to search getline string and replace it using getlineSeq string

$ sed ‘s/getline/getlineSeq/g’ sqio.c.bk > sqio.c

4. try to test using grep command

$ grep -n “getline” sqio.c

check output

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Mi Minuta Talleres Bioinformática Ciencias Genomicas UNAM 2012

Gracias a la invitación de Jerome Verleyne y Romualdo Zayas la cual agradezco mucho, participe como ponente en los talleres internacionales de bioinformática 2012 los cuales se llevaron a cabo en el Centro de Ciencias Genomicas de la UNAM del 16 al 27 de enero de 2012.

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my simple Galaxy script

Al trabajar con Galaxy y empezar a “indexar” los genomas de referencia para distintas herramientas NGS , me vi en la necesidad, en el caso de Blast, de complementar usando bash un script en python que permite preparar una base de datos para Blast en el formato adecuado para Galaxy.

Basicamente el flujo es:

Fasta File (in) – - > (process) – - > Galaxy Fasta File (out) – - > Blast Reference Seq

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