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84 results • Page
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Showing :
Parallel
•
reset
2
Votes
5
Replies
1.3k
Views
How about my parallel bwa+gatk pipeline?
gatk
parallel
pipeline
ngs
3.2 years ago
bluemonster0808
• 40
• updated 20 months ago
Charles Warden
6.8k
0
Votes
3
Replies
128
Views
Speed up psiblast of 11k alignments
psiblast
parallel
20 months ago
fhsantanna
• 440
0
Votes
1
Reply
148
Views
RepeatModeler contig size filter and parallelization
RepeatModeler
Contig length
Parallel
22 months ago
Anand Rao
• 210
3
Votes
4
Replies
812
Views
Parallel for bwa mem - problem with -R argument for ID and SM
parallel
alignment
bwa
2.9 years ago
Korsocius
• 110
• updated 22 months ago
ATpoint
17k
314
Votes
78
Replies
109k
Views
30 follow
Tool:
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
tools
parallel
next-gen
ngs
Tool
22 months ago
ole.tange
♦ 3.4k
1
Vote
7
Replies
291
Views
Snowfall Parallelisation to compute Correlation Matrix
snowfall
parallel
22 months ago
vincentpailler
• 50
5
Votes
3
Replies
339
Views
Best approach for parallelizing bwa mem over multiple CPUs
bwa
hpc
parallel
24 months ago
olikidrod
• 0
• updated 24 months ago
genomax
68k
7
Votes
10
Replies
1.7k
Views
6 follow
trying to use gnu parallel and blast
blast
parallel
gnu parallel
blastx
optimization
3.6 years ago
pablo61991
• 70
• updated 2.1 years ago
Giuseppe
• 0
2
Votes
2
Replies
1.3k
Views
GATK: -nct and -nt
gatk
parallel
3.8 years ago
fire_water
• 80
• updated 2.1 years ago
nick.carleson
• 10
12
Votes
0
Replies
547
Views
Tool:
Book: GNU Parallel 2018 - for beginners and advanced users
tool
ngs
parallel
Tool
2.2 years ago
ole.tange
♦ 3.4k
14
Votes
17
Replies
3.9k
Views
8 follow
Parallel Computing With Key/Value Stores (Multiple Writes)
parallel
database
9.8 years ago
Sequencegeek
• 740
• updated 2.3 years ago
amirouche.boubekki
• 10
10
Votes
2
Replies
3.9k
Views
Bwa: Number Of Threads
bwa
next-gen
sequencing
parallel
hardware
10.6 years ago
Pierre Lindenbaum
120k
• updated 2.4 years ago
RamRS
21k
3
Votes
16
Replies
1.7k
Views
How to let WGCNA use multiple cores
WGCNA
multe-thread
parallel
3.7 years ago
syrttgump
• 30
• updated 2.5 years ago
yplee614
• 0
3
Votes
13
Replies
1.3k
Views
Trim_galore on multiple fast.qz files: syntax problem
nsg
trim_galore
gnu
parallel
2.6 years ago
m93
• 150
2
Votes
2
Replies
469
Views
Are there any GNU parallel or similar Shell/Bash code examples on how to run Snap and BWA aligners on a batch of paired .fastq files?
gnu
parallel
shell
snap
bwa
2.8 years ago
england_bioinformatics_team
• 20
• updated 2.8 years ago
ATpoint
17k
2
Votes
3
Replies
519
Views
Are there any working GNU parallel or similar Shell code examples on how to run Pilon, Prokka, VT and Snpeff tools on a batch of input files?
gnu
shell
parallel
prokka
snpeff
2.8 years ago
england_bioinformatics_team
• 20
• updated 2.8 years ago
Joe
12k
5
Votes
9
Replies
3.2k
Views
Using parallel with Mem
mem
BWA
Parallel
6.8 years ago
always_learning
• 970
• updated 2.9 years ago
Korsocius
• 110
8
Votes
2
Replies
603
Views
Running assemblies in parallel
parallel
Assembly
fastq
3.0 years ago
marit.hetland
• 30
• updated 3.0 years ago
Joe
12k
0
Votes
1
Reply
390
Views
How to apply bedtools intersect function with GNU parallel for bacth BED file comparison?
bedtools
parallel
intersection
3.0 years ago
texaswhiskey1969
• 0
• updated 3.0 years ago
ATpoint
17k
0
Votes
2
Replies
492
Views
How to rewrite convert2bed function from BEDOps using GNU parallel for batch processing?
convert2bed
bedops
parallel
3.0 years ago
texaswhiskey1969
• 0
• updated 3.0 years ago
jean.elbers
♦ 1.1k
2
Votes
3
Replies
783
Views
Why can't I use a GRanges txDb with clusterMap function? (as input or output)
R
genomicFeatures
parallel
clusterMap
3.1 years ago
jhanks1981
• 0
2
Votes
2
Replies
561
Views
Paralellize samtools piped with awk
parallel
samtools
3.2 years ago
Korsocius
• 110
0
Votes
2
Replies
701
Views
How to increase the speed of miRanda target prediction program?
miranada
mirna
parallel
3.2 years ago
Vijay Lakhujani
4.1k
4
Votes
3
Replies
598
Views
Has anyone tried to run SNPEff, Bedtools or Prokka with GNU parallel or a similar batch engine?
gnu
parallel
snpeff
bedtools
prokka
3.2 years ago
bioinformatics_bel
• 20
• updated 3.2 years ago
WouterDeCoster
39k
5
Votes
0
Replies
801
Views
Tutorial:
Installing multiprocessor-capable MEME to work with a Slurm job scheduler environment
meme
slurm
parallelization
parallel
Tutorial
3.3 years ago
Alex Reynolds
28k
0
Votes
2
Replies
587
Views
What platform similar to Galaxy can handle multiple batch processing of bacterial genomes, mutation profiling and GWAS?
galaxy
platform
parallel
mutation profiling
gwas
3.5 years ago
bioinform
• 20
• updated 3.5 years ago
colindaven
♦ 1.3k
13
Votes
11
Replies
1.0k
Views
6 follow
Is it possible to run variant calling software in parallel, are there any Shell and Python/R code examples available?
parallel
vcf
variant calling
3.5 years ago
bioinform
• 20
• updated 3.5 years ago
ivivek_ngs
♦ 4.8k
2
Votes
3
Replies
657
Views
how to run obisplit in parallel
obitools
obisplit
parallel
linux
fastq
3.7 years ago
Roman Luštrik
• 70
5
Votes
4
Replies
1.5k
Views
parse error with samtools
samtools
linux
parallel
3.9 years ago
a.rex
• 190
2
Votes
4
Replies
1.1k
Views
Perl::ForkManager does not speed up ATCG calculation
Perl
Parallel
Speed
ForkManager
4.0 years ago
BioGeek
• 140
• updated 4.0 years ago
RamRS
21k
0
Votes
0
Replies
788
Views
PASTEC repeat classification software (part of REPET) help needed
repeat classification
repet
pastec
parallel
torque
4.0 years ago
mcsimenc
• 10
2
Votes
1
Reply
938
Views
Why trim_galore don't have parallel mode?
trim_galore
adaptor
parallel
4.1 years ago
Shicheng Guo
♦ 7.5k
5
Votes
2
Replies
1.4k
Views
Parallelizing MAFFT alignment of multiple FASTA files
alignment
mafft
parallel
4.4 years ago
ropolocan
• 520
3
Votes
7
Replies
1.2k
Views
parallel program for running a command for several files
parallel
Forum
4.5 years ago
prasoon.agarwal
• 10
• updated 4.5 years ago
Asaf
5.6k
8
Votes
5
Replies
855
Views
BLASTing very many 10-mers to human genome
cloud
parallel
blast
4.6 years ago
sor.hub.lennart
• 10
• updated 4.6 years ago
5heikki
8.4k
31
Votes
21
Replies
2.2k
Views
Job Manager to parallelize otherwise consecutive bash scripts..?
parallel
xargs
bash
5.0 years ago
John
12k
• updated 5.0 years ago
ole.tange
♦ 3.4k
4
Votes
5
Replies
1.8k
Views
How to use BBMap for aligning a set of .fastq files?
bbmap
bash
parallel
5.1 years ago
usgenome2018
• 30
• updated 5.1 years ago
Matt Shirley
9.0k
0
Votes
3
Replies
2.1k
Views
How to download multiple expression datasets from EBI database using ArrayExpress
ebi
microarray
parallel
5.2 years ago
deepue
• 110
• updated 5.2 years ago
genomax
68k
7
Votes
4
Replies
1.9k
Views
Running multiple instances of STAR in one directory
RNA-Seq
STAR
galaxy
parallel
5.3 years ago
Michael Dondrup
46k
3
Votes
14
Replies
1.8k
Views
Distributed (parallel) BLAST. Calculating E-values and other statistics params.
E-value
BLAST
Distributed
Parallel
bit-score
5.3 years ago
vladimir.khramkov
• 10
• updated 5.3 years ago
Damian Kao
15k
4
Votes
6
Replies
5.7k
Views
Cuffdiff Is Taking Forever. Can I Parallelize It?
cufflinks
cuffdiff
parallel
9.5 years ago
Ryan Thompson
♦ 3.4k
• updated 5.4 years ago
Biostar
20
4
Votes
1
Reply
1.8k
Views
seqtk trimfq in parallel fastx_trimmer
RNA-Seq
seqtk
parallel
5.6 years ago
syuja
• 20
15
Votes
18
Replies
16k
Views
8 follow
BLAST, setting maximum number of hits
BLAST
tblastx
parallel
5.9 years ago
apelin20
• 470
• updated 5.9 years ago
RamRS
21k
36
Votes
13
Replies
4.6k
Views
9 follow
Bioinformatics Tutorials Utilizing The Go ( Of Google Fame ) Programming Language
parallel
9.1 years ago
Delinquentme
• 200
• updated 6.0 years ago
Samuel Lampa
♦ 1.2k
2
Votes
7
Replies
1.1k
Views
Counting read spacing efficiently
sequencing
alignment
DNase-seq
parallel
6.0 years ago
André Rendeiro
• 50
• updated 6.0 years ago
Alex Reynolds
28k
2
Votes
1
Reply
1.7k
Views
Accelerating BLAST for million sequence BLASTp all-by-all
BLAST
parallel
cpu
mpi
6.0 years ago
Anand Rao
• 210
• updated 6.0 years ago
SES
8.2k
2
Votes
7
Replies
1.9k
Views
GNU Parallel Block Issues
blast
parallel
GNU parallel
block
6.1 years ago
salamayg
• 20
• updated 6.1 years ago
ole.tange
♦ 3.4k
1
Vote
1
Reply
1.4k
Views
VariantAnnotation parallel usage
R
bioconductor
parallel
6.2 years ago
russhh
♦ 4.4k
0
Votes
2
Replies
1.6k
Views
How to bind MPI parallel processes to specific cores
MPI
bind to core
parallel
6.2 years ago
Ginsea Chen
• 120
51
Votes
14
Replies
3.7k
Views
12 follow
How To Think In Parallel In Bioinformatics
parallel
10.2 years ago
Andrea_Bio
♦ 2.5k
• updated 6.2 years ago
ole.tange
♦ 3.4k
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