BenLangmead bowtie2 issues

BenLangmead / bowtie2

A fast and sensitive gapped read aligner

GNU General Public License v3.0

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issues

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Error: reads file does not look like a FASTQ file

#479 jtamames opened 3 weeks ago
0
Alignment performance decreases with higher `-p` option value

#478 LawrenceLiu023 opened 1 month ago
5
Alignment Question

#477 esdartez opened 1 month ago
0
--score-min and Deletion

#476 klxoo closed 1 month ago
0
--dpad --gbar

#475 zznx opened 1 month ago
2
--no-mixed --no-discordant

#474 zznx opened 1 month ago
1
Does the number of threads affect randomness?

#473 EReckase closed 1 month ago
2
Error, fewer reads in file specified with -1 than in file specified with -2

#472 abulislam opened 2 months ago
4
bowtie2-build only generate .3.bt2 and .4.bt2 two files

#471 cyundi opened 2 months ago
1
Question about pre-alignments

#470 h20gg702 opened 2 months ago
0
SAMflags to removes mapped concordantly >1 times

#469 Pompamm closed 2 months ago
4
Does End-to-End option override option with letter "L" ?

#468 santataRU closed 2 months ago
1
bowtie2 installed with Conda but failed to run due to "command not found"

#467 santataRU closed 4 months ago
1
paired-end reads align receive different when swap R1 with R2

#466 JBSScience opened 4 months ago
4
-p/--threads option always uses 1 more thread than is specified.

#465 leowill01 opened 4 months ago
1
bowtie2 with lower level of alignment when I align an assembly produced by two assemblers

#464 ksc289 opened 4 months ago
0
Error while flushing and closing output terminate called after throwing an instance of 'int' (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)

#463 Jingyniupp opened 5 months ago
7
Documenting Docker offerings

#462 jamesbraza opened 5 months ago
1
Added `CONTRIBUTING.md` explaining docs

#461 jamesbraza opened 5 months ago
1
How to edit docs?

#460 jamesbraza opened 5 months ago
2
Fix AVX2 build

#459 sfiligoi opened 5 months ago
0
Add --sam-omit-prim-seq

#458 sfiligoi closed 5 months ago
13
Add --omit-sec-seq

#457 wasade opened 5 months ago
0
Is option --n-ceil for reads only or also reference?

#456 AlineMuyle opened 6 months ago
2
putative error in CIGAR string

#455 pmjklemm closed 5 months ago
4
How to use -F option?

#454 bede opened 6 months ago
3
Linear memory consumption growth (with time) while aligning wgbs data using Bowtie2 >= 2.5.0

#453 iromeo opened 7 months ago
14
Index for metagenome

#452 jojyjohn28 opened 7 months ago
0
Paired-end bowtie2-align 2.5.2 crash when R2 fastq reads have been trimmed to zero length

#451 cnluzon opened 7 months ago
4
feature request: optional non-random selection among multiple best alignments

#450 eboyden opened 8 months ago
0
(ERR): bowtie2-align exited with value 134 (std::bad_alloc)

#449 Taurophylax opened 8 months ago
0
Support for Python 3.11 via Anaconda

#448 matthewfallan opened 8 months ago
4
Bowtie2 - Can't even get it to install!

#447 VariablePlant7 opened 9 months ago
1
stat: Bad file descriptor

#446 YuanChihLee closed 9 months ago
0
MQ scores are really low after using Bowtie2 with GATK

#445 hkarakurt8742 closed 8 months ago
2
something wrong when I install bowtie2.5.1 by anaconda

#444 Revolution233 opened 10 months ago
1
Different alignments in concatenated input vs comma-separated input

#443 jayrbolton opened 10 months ago
2
Feature request: another mode of "--un-mates"

#442 ZhangMH2000 closed 10 months ago
2
interleaved mode bug

#441 jianshu93 closed 8 months ago
4
"library not loaded error message in running test of bowtie2-build of bowtie2-2.5.1-macos-x86_64

#440 Rfriedmancolumbia opened 12 months ago
2
Identifying mapped locations of multi-mapped reads

#439 Sameerpython opened 1 year ago
0
Compiling from source only produces -debug binaries

#438 leannmlindsey opened 1 year ago
1
Increasing --threads increases execution time

#437 bede closed 8 months ago
11
Difference between single and paired end align strategy in bowtie2

#436 c4-driod opened 1 year ago
0
bowtie2-2.5.1-mingw-x86_64 does not support for compressed fastq files

#435 junjunlab closed 8 months ago
2
update SIMDe to v0.7.4

#434 mr-c closed 1 year ago
0
cmake produces identical bowtie-align-l and bowtie-align-s files

#433 OH-AU opened 1 year ago
4
Issues trying to make install bowtie2-2.2.2

#432 lateral-search closed 2 months ago
0
Building index of NCBI's Refseq bacterial genomes

#431 bheimbu opened 1 year ago
4
Bowtie2 (2.5.1) reported very different alignment rates with and without --no-mixed --no-discordant

#430 Ren-Meng opened 1 year ago
3