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116 results • Page
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Filtering for tag:
BBmap
•
reset
1
vote
5
replies
767
views
Efficient way to perform fastq filtering of contaminants by read name prior to transcriptome assembly?
trinity
BBmap
transcriptome
filtering
assembly
updated 4 days ago by
GenoMax
99k • written 5 days ago by
jfaberha
▴ 10
3
votes
0
replies
434
views
Tutorial:
Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap
Tutorial
11 weeks ago by
GenoMax
99k
6
votes
0
replies
1.1k
views
Tutorial:
Yes .. BBMap can do that! - Part II randomreads (read simulation), demuxbyname/filterbyname, bbsplit (read binning/decontamination) and pileup (cover…
bbmap
Tutorial
11 weeks ago by
GenoMax
99k
5
votes
0
replies
621
views
Tutorial:
Yes .. BBMap can do that! - Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)
bbmap
Tutorial
11 weeks ago by
GenoMax
99k
73
votes
79
replies
17k
views
17 follow
Tool:
Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.
compression
bbmap
clumpify
pigz
storage
Tool
updated 4 months ago by
wangpd35
• 0 • written 4.4 years ago by
Brian Bushnell
17k
8
votes
18
replies
271
views
BBMap tool error - randomreads.sh
software error
sequence
simulatedseq
bbmap
updated 4 months ago by
Ram
32k • written 4 months ago by
GLR
▴ 20
2
votes
2
replies
192
views
Dynamic string replacement issue in parallel for repair.sh bbmap
bbmap
gnu-parallel
4 months ago by
arunprasanna83
▴ 40
3
votes
7
replies
236
views
Tools for hard trimming?
bbmap
trimming
updated 4 months ago by
5heikki
9.7k • written 4 months ago by
v.berriosfarias
▴ 10
2
votes
5
replies
696
views
bbduk flags 'tossbrokenreads' and 'nullifybrokenquality'
BBMap
BBduk
flags
updated 5 months ago by
hegyihedi
• 0 • written 18 months ago by
Anand Rao
▴ 350
5
votes
10
replies
313
views
Estimaing insert size from a pair-end library using bbmap
RNA-Seq
bbmap
6 months ago by
Rogerio Ribeiro
▴ 50
0
votes
2
replies
228
views
VCFs appear inconsistent with view of alignment
vcf
gatk
freebayes
bbmap
igv
6 months ago by
mark.rose
▴ 40
1
vote
1
reply
249
views
BBDuk aggressive ktrim on ancient DNA samples
wgs
ancient DNA
BBMap
adapter trimming
updated 7 months ago by
GenoMax
99k • written 7 months ago by
ido.idobar
▴ 10
0
votes
5
replies
333
views
Please help about java error of BBDuk
bbmap
bbduk
java
brian bushnel
updated 17 days ago by
GenoMax
99k • written 7 months ago by
seta
★ 1.5k
4
votes
7
replies
351
views
bbduk.sh exceeding requested threads in an alignment pipeline
bbmap
hpc
7 months ago by
ido.idobar
▴ 10
0
votes
1
reply
317
views
Demuxbyname.sh dual index problem
demultiplex
demuxbyname.sh
bbmap
dual-index
8 months ago by
damt0320
• 0
0
votes
1
reply
228
views
BBnorm not outputting txt files when trying to determine ploidy on pb fastq.gz reads
kmer
khist
bbnorm
bbmap
ploidy
updated 8 months ago by
GenoMax
99k • written 8 months ago by
kristina.mahan
▴ 130
6
votes
9
replies
456
views
Split a FastQ file into smaller files
FastQ
bbmap
famas
awk
updated 8 months ago by
GenoMax
99k • written 8 months ago by
Matthias Zepper
▴ 70
0
votes
0
replies
281
views
NA match rate and high error rate with BBMap (mapPacBio)
Match rate
Nanopore
BBMap
mapPacBio
updated 10 months ago by
Biostar
20 • written 10 months ago by
elcombe.c
▴ 10
1
vote
4
replies
322
views
count reads (.sam) mapped to scaffolds with non-standard headers
sam
samtools
counts
bbmap
10 months ago by
rakshy
• 0
1
vote
2
replies
359
views
BBMap not indexing all chromosomes
BBMap
index
Error
10 months ago by
elcombe.c
▴ 10
0
votes
6
replies
740
views
Downsampling paired-end FASTQ files with a precise number of bases (not reads) - How to do it properly ?
ngs
FASTQ
downsampling
bbmap
10 months ago by
mikizu
• 0
1
vote
3
replies
290
views
How to use BBmap (mutate.sh) to simulate the human genome?
simulation
human genome
bbmap
updated 10 months ago by
Biostar
20 • written 11 months ago by
kamanovae
• 0
0
votes
5
replies
4.0k
views
Read trimming with BBDuk
bbduk
read trimming
bbmap
updated 10 months ago by
Biostar
20 • written 4.0 years ago by
seta
★ 1.5k
1
vote
2
replies
347
views
Mapping using assembled contigs
bbmap
mapping
assembly
contigs
genome
updated 11 months ago by
colindaven
★ 2.7k • written 11 months ago by
la_ff
• 0
0
votes
1
reply
253
views
Indexing vs Mapping
bbmap
index
mapping
11 months ago by
la_ff
• 0
2
votes
4
replies
323
views
BBmap: how to map ONLY paired-end reads to the reference
BBmap
updated 11 months ago by
GenoMax
99k • written 11 months ago by
b.shrestha
• 0
5
votes
11
replies
430
views
Filter fasta sequences based on a list with grep or BBmap
sequence
unix
linux
fasta
BBmap
11 months ago by
endretoth
▴ 20
0
votes
1
reply
330
views
bbMAP truncating problem: converting SAM to BAM?
RNA-Seq
alignment
bbmap
samtools
updated 12 months ago by
GenoMax
99k • written 12 months ago by
IzUSA
• 0
0
votes
0
replies
256
views
Mapping reads to repetitive positions in reference within edit distance and with 1 indel
bbmap
mapping
bowtie
12 months ago by
pawlowac
▴ 70
1
vote
5
replies
270
views
Reproducibility problem for BBduk between local server and HPC
reproducibility
HPC
bbmap
12 months ago by
DriesB
▴ 90
9
votes
5
replies
351
views
Snakemake and BBsplit.sh for filtrate human reads : memory management
snakemake
BBmap
13 months ago by
regue.hadrien
▴ 30
2
votes
9
replies
518
views
bbmap.sh: line 352 /random number/ Killed
bbmap
bbmap.sh: line 352 Killed
metagenome
updated 13 months ago by
GenoMax
99k • written 13 months ago by
mutantjoo0
• 0
1
vote
3
replies
405
views
bbsplit not using all reads in library
bbmap
bbsplit
bbduk
RNA-Seq
14 months ago by
ghd1998
• 0
19
votes
18
replies
6.8k
views
9 follow
Tool:
BBSketch - A Tool for Rapid Sequence Comparison
minhash
bbmap
blast
sketch
Tool
updated 15 months ago by
silas.kieser
• 0 • written 4.2 years ago by
Brian Bushnell
17k
0
votes
3
replies
371
views
BBNorm read depth binning behaviour inconsistent
bbmap
15 months ago by
Ben Anderson
• 0
2
votes
2
replies
500
views
BBmap caused Not in GZIP format
bbmap
sequencing
15 months ago by
Ric
▴ 350
3
votes
2
replies
556
views
How do I know how much memory to use when piping to with BBMap suite (OutOfMemoryError)?
bbmap
java
memory
reads
updated 15 months ago by
h.mon
32k • written 15 months ago by
O.rka
▴ 290
0
votes
3
replies
395
views
What does this code mean when using BBMap?
bbmap
metagenomics
16 months ago by
camerongubbins5
• 0
2
votes
3
replies
425
views
How to increase speed of BBMap's `reformat.sh` when randomly sampling reads?
RNA-Seq
sequencing
bbmap
fastq
16 months ago by
O.rka
▴ 290
1
vote
4
replies
523
views
bbmap reference mapping error
bbmap
mapping
java
error
updated 17 months ago by
ATpoint
47k • written 17 months ago by
drikaul
▴ 20
10
votes
6
replies
438
views
Interpreting bbduk histogram headers and contents
bbduk
bbmap
histograms
updated 17 months ago by
harold.smith.tarheel
★ 4.6k • written 17 months ago by
gnmcsbnfrmtcsclb
▴ 30
3
votes
5
replies
1.2k
views
Assembly statistics: ABySS & BBMap
assembly
abyss
bbmap
17 months ago by
el97004
▴ 40
6
votes
10
replies
693
views
BBmap pipeline output varies across replicated runs
bbmap
reproducibility
clumpify
17 months ago by
Anand Rao
▴ 350
1
vote
4
replies
1.4k
views
Bbmap filterbyname.sh to extract sequences out of a fasta file - wrong output
sequence extraction
bbmap
updated 18 months ago by
WouterDeCoster
45k • written 18 months ago by
marlenejensen
▴ 20
0
votes
0
replies
292
views
BBMap reformat.sh qahist statistics interpretation?
bbmap
18 months ago by
BioinformaticsLad
▴ 170
2
votes
2
replies
387
views
Suggestions for which genomes to use when removing microbial contamination with BBsplit
genome
BBmap
updated 18 months ago by
Biostar
20 • written 19 months ago by
Dave Carlson
▴ 610
0
votes
5
replies
473
views
How can I use BBMap reformat.sh to correctly retrieve fastq quality scores from a bam file?
software error
BBMap
reformat.sh
bam
quality
18 months ago by
thequokka
• 0
2
votes
2
replies
410
views
In the reformat tool of BBmap what is the meaning of Read1_linear and Read1_log
BBmap
quality
reads
updated 19 months ago by
h.mon
32k • written 19 months ago by
Joseph Hughes
★ 2.9k
0
votes
0
replies
426
views
Degenerate bases in reference and variant calling with bbmap callvariants.sh
bbmap
callvariants
19 months ago by
RSmith
• 0
0
votes
13
replies
1.7k
views
BBTools/BBMap/BBSuite's sketch.sh and sendsketch.sh are inconsistent
bbmap
kmer
sketch
bbtools
bbsuite
20 months ago by
O.rka
▴ 290
116 results • Page
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