cinvestav

Research projects

Cluster de Cómputo de Alto Rendimiento "Mazorka"



 

Infraestructura

 

Queue anterior

Queue

Nodos (prendidos)

Proc / Nodo

Núcleos / Proc

Núcleos / Nodo

RAM [GB/Nodo]

Procesador

TFLOPS / Queue

ensam

ensam

2 (2)

32

260

E7-4820  @ 2.00GHz

0.512 

biofis

default

8 (8)

12

24

X5675  @ 3.07GHz

1.179 

mem64

default

4 (4)

8

64

E5530  @ 2.40GHz

0.307 

quad

default

30 (26)

8

24

E5530  @ 2.40GHz

2.304 

twin

default

12 (2)

8

16

E5462  @ 2.80GHz

1.075 

xeon

default

10 (0)

1

2

2

8

Xeon @ 3.20GHz

0.256 

TOTAL

66 (42)

 

 

532

 

 

 5.633


Link a la página del Cluster Híbrido de Supercómputo - Xiuhcoatl - Cinvestav 

 

 

 

Aplicaciones

 

Nombre

Versión

Descripción

abyss

-1.3.4

Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler 

amos

-3.1.0

A Modular, Open-Source whole genome assembler

b2g4pipe235

 

ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data

BioPerl

-1.6.1

 Perl code which is useful in biology.

blast

-2.2.26

BLAST finds regions of similarity between biological sequences 

bowtie2

-2.0.0-beta3

Bowtie is an ultrafast, memory-efficient short read aligner 

bwa

-0.6.2

Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome 

CAP3

 

Sequence Assembly Program 

clustalw

-2.0.12

Multiple alignment of nucleic acid and protein sequences 

EMBOSS

-6.4.0

EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology 

fastq_screen

_v0.2.1

 FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect

fastx_toolkit

-0.0.13

The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.  

gatk

2.2-8

The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance 

genometools

-1.3.9

The versatile open source genome analysis software 

gmap-gsnap

-2012-07-20

A Genomic Mapping and Alignment Program for mRNA and EST Sequences 

gromacs

-4.5.5

GROMACS is a versatile package to perform molecular dynamics 

hmmer3

 

Biosequence analysis using profile hidden Markov models

LifeScope

 

 

mauve

_2.3.1

 

MEGAN_unix

_3_9.sh

MEGAN ('MEtaGenome ANalyzer') is a computer program that allows optimized analysis of large metagenomic datasets 

meme

_4.4.0

Motif-based sequence analysis tools

mira

3.2

MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio 

Mosaik

-1.1.0021-Linux-x64

MOSAIK is a reference-guided assembler comprising of four main modular programs 

mrbayes

_3.2.1

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models

MUMmer

3.23

Ultra-fast alignment of large-scale DNA and protein sequences 

muscle

3.8.31_i86linux64

Multiple sequence alignment 

NAMD

_2.8b1_Source

A parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems

ncbi-blast

-2.2.26+

BLAST finds regions of similarity between biological sequences 

orthologid

 

OrthologID automates gene orthology determination within a character-based phylogenetic framework 

pcap

linux.64

Assembly Program

phylobayes

3.2d

PhyloBayes is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction 

phyml

v3.0

PhyML is a phylogeny software based on the maximum-likelihood principle 

piler

 

Genomic repeat analysis software 

prottest

-3

High performance computing application for amino-acid model selection 

PyRosetta

-Release1.1-r34968

Interactive Molecular Modeling for Proteins 

R

-2.15.0

Statistical Computing 

RECON

1.06

A package for automated de novo identification of repeat families from genomic sequences 

RepeatMasker-open

-3-3-0

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences 

RepeatModeler

-1-0-4

epeatModeler is a de-novo repeat family identification and modeling package 

RepeatScout

-1.0.5

RepeatScout is a tool to discover repetitive substrings in DNA 

REPET

_linux-x64_2.0

The REPET package integrates bioinformatics programs in order to tackle biological issues at the genomic scale 

rmblast

-1.2-ncbi-blast-2.2.23+

RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite 

rosetta

3.1_MPI

ROSETTA is a software suite for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions. 

samtools

-0.1.18

SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments

SOAPdenovo

-v1.04

SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes 

SOPRA

_v1.3.2

Assembler for mate pair/paired-end reads from high throughput sequencing platforms, e.g. Illumina and SOLiD 

sspace

 

SSPACE is a stand-alone program for scaffolding pre-assembled contigs using paired-read data

structure

 

The program structure is a free software package for using multi-locus genotype data to investigate population structure 

trinity

r2012-10-05

Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.

vcake

 

VCAKE is a genetic sequence assembler capable of assembling millions of small nucleotide reads even in the presence of sequencing error 

velvet

_1.1.03

Sequence assembler for very short reads 

wgs

-6.1

Celera Assembler is a de novo whole-genome shotgun (WGS) DNA sequence assembler 

wise

02/04/01

The Wise2 form compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors. 

XSQ_Tools

_20120109

 







For more information, contact: Mauricio Carrillo Tripp

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