ababaian/serratus

Issues

• all serratus assemblies (60k accessions)

  #260 opened 3 years ago by rchikhi
  13

• Serratus-Lite summarizer script

  #278 opened 8 months ago by TWilson1012
  2

• BUG rows on srarun missing values on the spots column

  #277 opened a year ago by almosnow
  1

• question about cloud budget

  #276 opened a year ago by charlie2021cc
  1

• Adding new column to the Serratus search?

  #275 opened a year ago by mmsonder
  1

• scRNA-seq analysis with Serratus

  #274 opened a year ago by malonzm1
  1

• Website is down

  #273 opened a year ago by austinreidmanny
  2

• Tree data

  #272 opened 2 years ago by ellasiera
  2

• Bug in the SRA meta-data analysis from palmID

  #271 opened 2 years ago by PuravG
  0

• additional things to migrate to lovelywater:

  #266 opened 2 years ago by rchikhi
  0

• palmID viral RdRp analysis crash

  #265 opened 2 years ago by FBeguier
  10

• Is Serratus running on most recent SRAs?

  #263 opened 3 years ago by centaria
  4

• Speed up SRA download: aws s3 cp or sratoolkit?

  #262 opened 3 years ago by centaria
  7

• Novel viruses identified by Serratus

  #261 opened 3 years ago by aninditaces
  2

• Hello! Many parts of this tutorial “Running Serratus”are confusing to me. Could you be more specific?

  #259 opened 3 years ago by NickShanyt
  6

• Phylogenetic and taxonomic analyses for any viral contigs

  #258 opened 3 years ago by eul2021
  5

• Download fasta file

  #257 opened 3 years ago by MjelleLab
  10

• Brief SRA metadata for a subset of SRR ids

  #256 opened 3 years ago by eul2021
  3

• Deal with suppressed phage runs

  #255 opened 3 years ago by taltman
  1

• Migrate improved CoV assemblies to lovelywater, and annotate them

  #254 opened 3 years ago by taltman
  0

• assemblies of 1k random SRAs from novel_id90.fa

  #246 opened 4 years ago by rchikhi
  10

• Migrate assembly data to lovelywater

  #237 opened 4 years ago by ababaian
  23

• all RdRP+ macro/micro contigs

  #252 opened 4 years ago by rchikhi
  1

• Update contributors list

  #250 opened 4 years ago by victorlin
  1

• migrate RdRP data to lovelywater

  #251 opened 4 years ago by rchikhi
  5

• Canonicalize assembly ordering and orientation

  #216 opened 4 years ago by taltman
  8

• TODO: Case study for CoV in environmental samples

  #248 opened 4 years ago by ababaian
  0

• all new nido/cov assemblies

  #247 opened 4 years ago by rchikhi
  2

• all .pro assemblies

  #242 opened 4 years ago by rchikhi
  10

• Please run SRA SRR11085797

  #243 opened 4 years ago by bioscienceresearch
  4

• Please run SRR12432009

  #245 opened 4 years ago by bioscienceresearch
  0

• Please Run SRA SRR11806578

  #244 opened 4 years ago by bioscienceresearch
  0

• rVert assemblies

  #241 opened 4 years ago by rchikhi
  5

• Dicistro assemblies

  #239 opened 4 years ago by rchikhi
  16

• Summary file version inconsistencies

  #240 opened 4 years ago by victorlin
  3

• Quenya assemblies

  #238 opened 4 years ago by rchikhi
  5

• Discrepancy in counting RdRp hits in SRR11648360

  #228 opened 4 years ago by taltman
  1

• Extracting genome structure [from Darth, or not]

  #226 opened 4 years ago by rchikhi
  18

• Align poly-A tail reads against assembly to identify putative 3' of genome

  #222 opened 4 years ago by taltman
  3

• Create ranked list of BioProjects for Co-Assembly

  #217 opened 4 years ago by taltman
  6

• PFAM alignments for Toro outgroup

  #215 opened 4 years ago by rcedgar
  9

• Procedure to construct assembly-host association table

  #219 opened 4 years ago by rcedgar
  1

• Plan for Fig 1 for discussion on July 24th status call

  #225 opened 4 years ago by rcedgar
  4

• Expand the set of Nidovirales-associated Pfam HMMs for contig identification

  #231 opened 4 years ago by taltman
  2

• Develop Nido HMM library for genome annotations

  #227 opened 4 years ago by rcedgar
  21

• Assemblies were updated (7/28) due to two bugs

  #230 opened 4 years ago by rchikhi
  7

• OTU pipeline must delete '.' insertion character from Pfam a2m-formatted output produced by darth

  #229 opened 4 years ago by taltman
  1

• Capture multiple RdRp's from one assembly

  #223 opened 4 years ago by rcedgar
  28

• PFAM alignment bug

  #224 opened 4 years ago by rcedgar
  11

• Filter Ion Torrent (other?) from OTU table

  #218 opened 4 years ago by rcedgar
  20