marbl/SALSA

Issues

• Similar number of scaffolds to contigs

  #182 opened 5 months ago by dgs108
  2

• AGP file has 500bp gaps labelled as "scaffold" with linkage asserted but "na" given for linkage evidence

  #179 opened 7 months ago by dgs108
  1

• Single Restriction Enzyme Used for HiC Preparation

  #180 opened 8 months ago by foreignsand
  0

• Hi-C links not loading

  #175 opened 10 months ago by sanalbert
  4

• Improving Trio-binning assembly using SALSA2

  #177 opened 10 months ago by Larkinhi
  5

• If a FASTA file has “V” sequence, the following error occurred

  #171 opened 10 months ago by c2997108
  1

• How to get Python3 supported version?

  #149 opened 10 months ago by xiekunwhy
  1

• Representation of broken contigs in FINAL.agp file

  #176 opened 10 months ago by woodoo46
  1

• Output scaffolds_FINAL.fasta is binary

  #174 opened a year ago by mkyriak
  0

• Generate <*.hic> file using a parallel option?

  #173 opened 2 years ago by cement-head
  1

• Generating .hic file with convert.sh

  #138 opened 4 years ago by kishor2019
  4

• Assembly does not improve

  #172 opened 2 years ago by gubrins
  3

• Please explain: -i ITER, --iter ITER Number of iterations to run, default = 3

  #131 opened 2 years ago by ckeeling
  1

• Two HiC experiments: recommend combine data or run SALSA sequentially?

  #133 opened 2 years ago by ckeeling
  2

• Mate-pair in SALSA

  #170 opened 2 years ago by aabaricalla
  1

• Salsa stopping iterating a bit too soon ?

  #169 opened 2 years ago by vpymerel
  0

• Arima 2-enzymes restriction site (^GATC and G^ANTC)

  #168 opened 2 years ago by edanchin
  2

• 'Error in generated code:', file=sys.stderr

  #155 opened 2 years ago by SchwarzEM
  6

• fatal error: boost/config.hpp: No such file or directory

  #167 opened 2 years ago by Surbhigrewal
  2

• No scaffols_FINAL file

  #166 opened 2 years ago by gubrins
  2

• No Change in Assembly stats after HiC salsa

  #158 opened 3 years ago by shaferab
  3

• possible to phase haplotypes?

  #159 opened 2 years ago by zhaotao1987
  2

• USing SALSA to scaffold a CANU CLR PacBio reads assembly

  #163 opened 2 years ago by aureliendejode
  3

• no scaffold assembly, the assembly stats is no change

  #164 opened 2 years ago by guo-cheng
  2

• correct_links: Aborted

  #165 opened 2 years ago by guo-cheng
  1

• YAHS

  #162 opened 3 years ago by larryns
  2

• scaffold orientation

  #157 opened 3 years ago by olechnwin
  3

• Does SALSA use multiple threads/cores?

  #160 opened 3 years ago by romseg
  1

• convert.sh does not produce a .hic file in the appropriate format for juicebox

  #154 opened 3 years ago by oneillkza
  7

• Proximo Hi-C (Phase Genomics)

  #135 opened 3 years ago by carolhsb
  3

• Why do I still get misassembles thought salsa didn't find any?

  #156 opened 3 years ago by zmz1988
  1

• Grouping scaffolds into chromosomes

  #152 opened 3 years ago by kkrizanovic
  1

• Would it be possible to get convert.sh and its dependencies included in the conda environment/container?

  #153 opened 3 years ago by oneillkza
  0

• Number of iterations different than stated

  #151 opened 3 years ago by CIWa
  3

• How to set RE_site?

  #150 opened 3 years ago by xingchang-web
  1

• marking duplicates

  #146 opened 3 years ago by olechnwin
  1

• minimap aligner

  #147 opened 3 years ago by sammywinchester19
  1

• Can software assemble genomes at the chromosome level

  #145 opened 3 years ago by ld9866
  6

• Restriction sites where the cut-site is in the middle.

  #144 opened 3 years ago by DustinSokolowski
  2

• About plot in your article

  #143 opened 3 years ago by zhoudreames
  1

• Forcing merge of scaffolds

  #129 opened 4 years ago by chopra29
  1

• break_contigs_start: not found

  #132 opened 3 years ago by Lattesnow
  3

• Omni-C

  #141 opened 3 years ago by ardy20
  1

• Numpy Requirement

  #136 opened 3 years ago by aakashsur
  1

• ImportError: No module named networkx

  #142 opened 3 years ago by khush876
  1

• KeyError:

  #140 opened 4 years ago by kalbflei
  2

• Still runs with empty bed

  #137 opened 4 years ago by aakashsur
  0

• sorting bed file

  #134 opened 4 years ago by kishor2019
  2

• Post processing steps after SALSA

  #128 opened 4 years ago by pubudumanoj
  1

• white gaps and serial numbered scaffolds in SALSA outputs

  #125 opened 4 years ago by Smediterranea
  0