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ababaian
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serratus
Ultra-deep search for novel viruses
http://serratus.io
GNU General Public License v3.0
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Discrepancy in counting RdRp hits in SRR11648360
#228
taltman
closed
3 years ago
1
Develop Nido HMM library for genome annotations
#227
rcedgar
opened
3 years ago
21
Extracting genome structure [from Darth, or not]
#226
rchikhi
closed
3 years ago
18
Plan for Fig 1 for discussion on July 24th status call
#225
rcedgar
closed
3 years ago
4
PFAM alignment bug
#224
rcedgar
closed
3 years ago
11
Capture multiple RdRp's from one assembly
#223
rcedgar
closed
3 years ago
28
Align poly-A tail reads against assembly to identify putative 3' of genome
#222
taltman
closed
3 years ago
3
Notebooks, genome_metadata.py and sra_metadata.py
#221
taltman
closed
3 years ago
2
Update serratus_assembly_minimap2_qc.py
#220
rcedgar
closed
3 years ago
0
Procedure to construct assembly-host association table
#219
rcedgar
closed
3 years ago
1
Filter Ion Torrent (other?) from OTU table
#218
rcedgar
closed
3 years ago
20
Create ranked list of BioProjects for Co-Assembly
#217
taltman
closed
3 years ago
6
Canonicalize assembly ordering and orientation
#216
taltman
closed
3 years ago
8
PFAM alignments for Toro outgroup
#215
rcedgar
closed
3 years ago
9
A portion of the master table assemblies will be re-run/re-annotated
#214
rchikhi
closed
3 years ago
9
Missing RdRP domain in assembly annotations
#213
rcedgar
closed
3 years ago
14
Assemblies with >1 Cov
#212
rcedgar
opened
3 years ago
8
Run annotation pipeline on 99% nt OTUs
#211
rcedgar
closed
3 years ago
2
Host-virus tables
#210
rcedgar
closed
3 years ago
0
serraplace update for richer output / simpler best per-query output
#209
pierrebarbera
closed
3 years ago
0
Add vim, less, bash_include to serratax Dockerfile
#208
rcedgar
closed
3 years ago
0
Use 97% RdRp a.a. identity for species OTUs
#207
rcedgar
closed
3 years ago
2
Additional PFAM alignments
#206
rcedgar
closed
3 years ago
7
DARTH: Uninitialized value error from VADR
#205
taltman
closed
3 years ago
9
Re-build seq/cov5 99% nt redundancy set to prioritize RefSeqs
#204
rcedgar
closed
3 years ago
9
Genbank records missing PFAM annotations
#203
rcedgar
closed
3 years ago
7
Combine host-virus association databases into one tsv file
#202
rcedgar
closed
3 years ago
18
Missing fasta alignments in darth output
#201
rcedgar
closed
3 years ago
9
Placement dev update
#200
pierrebarbera
closed
3 years ago
0
Fix missing SERRATAX_LIBDIR bug
#199
rcedgar
closed
3 years ago
0
Update README.md
#198
rcedgar
closed
3 years ago
0
Selection of assemblies into master table (category, filtering method)
#197
rchikhi
closed
3 years ago
10
Identify characteristic domains in Cov genomes
#196
rcedgar
closed
3 years ago
37
Designate assemblies as putative new species or new genus
#195
rcedgar
closed
3 years ago
2
OTU and tree construction for Fig. 1
#194
rcedgar
closed
3 years ago
1
Data Compliation 1: CoV master table
#193
ababaian
closed
3 years ago
17
Migrate serratax python code to github repo
#192
rcedgar
closed
3 years ago
0
Come up with source organism description for each genome
#191
taltman
opened
3 years ago
4
Get NCBI BioProject ID
#190
taltman
opened
3 years ago
1
Create template.sbt metadata file for batch tbl2asn submission
#189
taltman
opened
3 years ago
2
Add tbl2asn branch to Darth pipeline
#188
taltman
opened
3 years ago
0
Specific annotation requirements for viral TPA submissions
#187
taltman
opened
3 years ago
9
Viral metadata needed for GenBank submission
#186
taltman
opened
3 years ago
0
Report of July 8th assemblies (1.3k datasets)
#185
rchikhi
closed
3 years ago
14
serratax bug when query falls outside all genera
#184
rcedgar
closed
3 years ago
6
Downstream analysis of assemblies
#183
rcedgar
opened
4 years ago
7
Add avgcols=xxx
#182
rcedgar
closed
4 years ago
0
Sumzer updates
#181
rcedgar
closed
4 years ago
0
Placement dev update
#180
pierrebarbera
closed
3 years ago
1
Update serratus_assembly_minimap2_qc.py
#179
rcedgar
closed
4 years ago
0
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