Skip to content

Issues: BenLangmead/bowtie2

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Clear current search query, filters, and sorts
159 Open 276 Closed
159 Open 276 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Issues list

mapping bias for multimapped reads
#20 opened Mar 18, 2015 by val-antonescu
Please clarify the "alignment summary"
#125 opened Jul 24, 2017 by rotifergirl
question about aligning pairs in bowtie2
#168 opened Dec 29, 2017 by Yuxuan0060
Suggestion to improve user manual
#219 opened Nov 7, 2018 by TrentBrick
Recommended options for metagenomic assembly?
#222 opened Jan 11, 2019 by louellette
Small patch for portability
#236 opened Mar 17, 2019 by outpaddling
feature requests: support for graph genomes, full IUPAC code, SNP-aware alignment
#237 opened Mar 18, 2019 by eboyden
precedent of parameters when using a preset
#242 opened Apr 2, 2019 by romunov
Feature request- allow user to specify a temp dir
#258 opened Jul 16, 2019 by ijhoskins
bowtie2-align exited with value 134
#261 opened Aug 26, 2019 by ZhihengVincentLiu
using redundant database
#272 opened Dec 25, 2019 by alaraints
bowtie2 does not work
#273 opened Dec 27, 2019 by danich64
anomalous bowtie2 alignment
#276 opened Jan 30, 2020 by rosema62
Invalid double quote character is used in the code
#278 opened Feb 28, 2020 by junaruga
XS score in secondary alignments
#281 opened Mar 16, 2020 by fxjonas
"\1 better written as $1" warnings in simple_tests.pl
#288 opened Apr 13, 2020 by junaruga
Variability in length of resulting scaffold
#313 opened Sep 25, 2020 by LauraVP1994
Report all "equally-best" alignments for a given read
#319 opened Nov 11, 2020 by apcamargo
Bail out sooner if numbers of paired ends don't match
#328 opened Dec 16, 2020 by GloverLab
bug report
#338 opened Apr 1, 2021 by KihongHeo
Migrate Travis CI by May 31, 2021
#339 opened May 8, 2021 by junaruga
@ch4rr0
bowtie2 on GPU?
#358 opened Oct 19, 2021 by GeoMicroSoares
Select local alignment or end-to-end alignment for filtering rRNA
#362 opened Nov 28, 2021 by Duannai
--passthrough with --sam-append-comment
#363 opened Dec 2, 2021 by MikeWLloyd
Missing Discussion of Alternate Contigs in Manual
#373 opened Feb 15, 2022 by DarioS
ProTip! Mix and match filters to narrow down what you’re looking for.