Hileko artxiboak: September 2015

Qbox

Uncategorized @eu

Informazio Orokorra

Bertsioa: 1.62.3

Qbox is a C++/MPI scalable parallel implementation of first-principles molecular dynamics (FPMD) based on the plane-wave, pseudopotential formalism. Qbox is designed for operation on large parallel computers.

Nola Erabili

Lanak bidaltzeko send_qbox tresna prestatu dugu honako erabilerarekin:

send_qbox JOBNAME NODES PROCS_PER_NODE[property] TIME

send_box [Enter] egikarituta erabilgarri dauden beste hainbat aukera erakutsiko dira. Programa /software/qbox katalogoan dago kokatuta.

Informazio Gehiago

Qbox Web orrialdea.

IDBA-UD

Genetika, Kalkulu Softwarea

Informazio orokorra

IDBA-UD 1.1.1 is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth contigs are removed iteratively with cutoff threshold from low to high to reduce the errors in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD can iterate k value of de Bruijn graph to a very large value with less gaps and less branches to form long contigs in both low-depth and high-depth regions.

Nola erabili

Lanak koletara bidaltzeko ondorengo komandoa erabili daiteke

send_idba-ud

eta galdera batzuk erantzun eta gero bidaliko du lana.

Erendimendua

IDBA-UD ondo eskalatzen du 8 koreetaraino. Hortik gora ez dugu inongo hobenkuntzarik nabaritu. Benchmark --mimk 40 --step 20 aukerekin egin da eta step murriztu dugunean okerrago paralelizatzen du. Bigarren taulan ere step 10-ekin errendimendua ez da ona 4 koretik gora.

kore 1 oinarri bezala 2 kore oinarri bezala
Koreak Denbora (s) Azelerazioa Errendimendua (%) Azelerazioa Errendimendua
1 480 1 100
2 296 1.6 81 1.0 100
4 188 2.6 64 1.6 79
8 84 5.7 71 3.5 88
12 92 5.2 43 3.2 54

Bigarren benchmarka fitxategin handiago batekin egin dugu, 10 milio basetakoa eta --mink 20 --step 10 --min_support 2 aukerekin. Ikusten dugu konportamendu erregularragoa eta nola 4 koreetatik gora ez duen ondo eskalatzen.

Koreak Denbora (s) Azelerazioa errendimendua (%)
1 13050 1 100
2 6675 2.0 98
4 3849 3.4 85
8 3113 4.2 52
16 2337 5.6 35
20 2409 5.4 27

Informazio gehigo

IDBA-UD web orrialdea.

SPAdes

Genetika

Informazio orokorra

SPAdes 3.6.0 – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. It works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. You can also provide additional contigs that will be used as long reads. Supports paired-end reads, mate-pairs and unpaired reads. SPAdes can take as input several paired-end and mate-pair libraries simultaneously. Note, that SPAdes was initially designed for small genomes. It was tested on single-cell and standard bacterial and fungal data sets.

Nola erabili

Kalkuluak bidaltzeko koletara

send_spades

komandoa erabili daiteke, honek galdera batzuk erantzutez kalkulua konfiguratuko du.

Errendimendua

Ez da neurtu inongo hobekuntzarik hainbat koreak erabiliz kalkulu normal batean, mota henetakoa:

spades.py -pe1-1 file1 -pe1-2 file2 -o outdir

Kore bakarra erabiltzea gomendatzen dugu, errendimendu hobea lortuko dela jakin ezik kore gehiago erabiliz gero.

Informazio gehiago

SPAdes web orrialdea.