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nf-core
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ampliseq
Amplicon sequencing analysis workflow using DADA2 and QIIME2
https://nf-co.re/ampliseq
MIT License
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Prevent masking low complexity regions by VSEARCH
#679
d4straub
closed
9 months ago
2
Debug information for docker-based run.
#678
hh1985
closed
9 months ago
4
Update sbdiexport
#677
jtangrot
closed
9 months ago
1
Fix phyloseq input
#676
d4straub
closed
9 months ago
2
Add Zehr nifH database
#675
erikrikarddaniel
closed
9 months ago
1
Add PhytoRef
#674
erikrikarddaniel
closed
9 months ago
2
Fix qiime2 taxonomy part of summary report using unavailable information.
#673
MatthewJM96
closed
9 months ago
2
Update output docs for collapsed abundance tables
#672
danclaytondev
closed
10 months ago
4
Update Output Docs for Collapsed Abundance Tables
#671
danclaytondev
closed
10 months ago
1
Add option to assign ASV to multiple species with DADA2
#670
andand
closed
9 months ago
3
Allow to analyse 454 sequencing data
#669
d4straub
opened
10 months ago
2
Edge case: Clustering with VSEARCH fails at QIIME2_INSEQ
#668
d4straub
closed
9 months ago
1
Added QIIME2 custom reference database support.
#667
MatthewJM96
closed
9 months ago
10
Greengenes2 2022.10 Support
#666
MatthewJM96
closed
8 months ago
5
Add custom qiime reference database support to Ampliseq.
#665
MatthewJM96
closed
9 months ago
2
Add greengenes2 2022.10 support to Ampliseq
#664
MatthewJM96
closed
10 months ago
1
Add blast-consensus support to Ampliseq
#663
MatthewJM96
opened
10 months ago
1
Phyloseq object creation will fail if any samples have all reads removed by the tax filtering step
#662
agrier-wcm
closed
10 months ago
5
Bump version 2.7.1 to 2.8.0dev
#661
d4straub
closed
10 months ago
5
Release 2.7.1
#660
d4straub
closed
10 months ago
2
Prepare release 2.7.1
#659
d4straub
closed
10 months ago
1
Adding the new Greengenes2 database for classification
#658
aimirza
opened
10 months ago
17
Improve reporting
#657
d4straub
closed
10 months ago
1
Move conda check to script section
#656
d4straub
closed
10 months ago
2
Fix nextflow version 23.10.0 with QIIME2
#655
d4straub
closed
10 months ago
2
Nextflow version 23.10.0 is incompatible with QIIME2 (pipeline fails), solution: prepend 'NXF_VER=23.04.4' when running the pipeline
#654
bioinfogaby
closed
10 months ago
17
I didn't receive an email notification
#653
luozhy88
closed
11 months ago
3
Report shows wrong taxonomic classification stats for QIIME with UNITE
#652
d4straub
closed
10 months ago
3
Bump version to 2.8.0dev
#651
d4straub
closed
11 months ago
2
Requirement Exceeds Available Memory for CUTADAPT
#650
aqsakhalid03
closed
11 months ago
7
CUTADAPT Workflow error
#649
aqsakhalid03
closed
11 months ago
5
Release 2.7.0
#648
d4straub
closed
11 months ago
2
Prepare 2.7.0 release
#647
d4straub
closed
11 months ago
2
Update dependencies
#646
d4straub
closed
11 months ago
2
Update workflow overview figure & docs
#645
d4straub
closed
11 months ago
1
Update pipeline summary report
#644
d4straub
closed
11 months ago
1
Fix --dada_ref_tax_custom without --dada_ref_tax_custom_sp
#643
d4straub
closed
1 year ago
2
Merging template updates 2.10
#642
d4straub
closed
1 year ago
2
Continue analysis even when individual files fail the filtering threshold
#641
sminot
closed
1 year ago
5
Important! Template update for nf-core/tools v2.10
#640
nf-core-bot
closed
1 year ago
0
Add GTDB 214.1 for DADA2
#639
d4straub
closed
1 year ago
1
Catch error case where 0 reads pass filtering and params.ignore_failed_trimming = True
#638
sminot
closed
1 year ago
8
Add taxonomic classification with kraken2
#637
d4straub
closed
1 year ago
2
Adding gtdb release 214 & adding already downloaded database
#636
x-rv
closed
1 year ago
2
Broken link in README.md
#635
a4000
closed
1 year ago
2
A feature to remove taxa found in controls
#634
skose82
opened
1 year ago
5
disable GPU for UNIFRAC
#633
d4straub
closed
1 year ago
2
Add alpha diversity to sample count correlation to report
#632
d4straub
closed
1 year ago
2
Add vsearch uchime_denovo for chimera removal (or flagging)
#631
andand
opened
1 year ago
2
Fix filters with --input_fasta
#630
d4straub
closed
1 year ago
4
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