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marbl
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SALSA
SALSA: A tool to scaffold long read assemblies with Hi-C data
MIT License
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Similar number of scaffolds to contigs
#182
dgs108
opened
2 months ago
2
update AGP
#181
skoren
closed
4 months ago
0
Single Restriction Enzyme Used for HiC Preparation
#180
foreignsand
closed
5 months ago
0
AGP file has 500bp gaps labelled as "scaffold" with linkage asserted but "na" given for linkage evidence
#179
dgs108
closed
4 months ago
1
fix IUPAC
#178
skoren
closed
4 months ago
0
Improving Trio-binning assembly using SALSA2
#177
Larkinhi
closed
7 months ago
5
Representation of broken contigs in FINAL.agp file
#176
woodoo46
closed
7 months ago
1
Hi-C links not loading
#175
sanalbert
closed
7 months ago
4
Output scaffolds_FINAL.fasta is binary
#174
mkyriak
opened
1 year ago
0
Generate <*.hic> file using a parallel option?
#173
cement-head
opened
1 year ago
1
Assembly does not improve
#172
gubrins
opened
1 year ago
3
If a FASTA file has “V” sequence, the following error occurred
#171
c2997108
closed
7 months ago
1
Mate-pair in SALSA
#170
aabaricalla
closed
1 year ago
1
Salsa stopping iterating a bit too soon ?
#169
vpymerel
opened
2 years ago
0
Arima 2-enzymes restriction site (^GATC and G^ANTC)
#168
edanchin
closed
2 years ago
2
fatal error: boost/config.hpp: No such file or directory
#167
Surbhigrewal
closed
2 years ago
2
No scaffols_FINAL file
#166
gubrins
closed
2 years ago
2
correct_links: Aborted
#165
guo-cheng
opened
2 years ago
1
no scaffold assembly, the assembly stats is no change
#164
guo-cheng
closed
2 years ago
2
USing SALSA to scaffold a CANU CLR PacBio reads assembly
#163
aureliendejode
closed
2 years ago
3
YAHS
#162
larryns
closed
2 years ago
2
added -O for original coordinates agp
#161
pickettbd
closed
2 years ago
0
Does SALSA use multiple threads/cores?
#160
romseg
closed
2 years ago
1
possible to phase haplotypes?
#159
zhaotao1987
closed
2 years ago
2
No Change in Assembly stats after HiC salsa
#158
shaferab
closed
2 years ago
3
scaffold orientation
#157
olechnwin
closed
2 years ago
3
Why do I still get misassembles thought salsa didn't find any?
#156
zmz1988
opened
2 years ago
1
'Error in generated code:', file=sys.stderr
#155
SchwarzEM
closed
2 years ago
6
convert.sh does not produce a .hic file in the appropriate format for juicebox
#154
oneillkza
opened
2 years ago
7
Would it be possible to get convert.sh and its dependencies included in the conda environment/container?
#153
oneillkza
opened
2 years ago
0
Grouping scaffolds into chromosomes
#152
kkrizanovic
opened
2 years ago
1
Number of iterations different than stated
#151
CIWa
opened
3 years ago
3
How to set RE_site?
#150
xingchang-web
closed
3 years ago
1
How to get Python3 supported version?
#149
xiekunwhy
closed
7 months ago
1
Moved to python 3 and Networkx 2.6
#148
pintomollo
opened
3 years ago
0
minimap aligner
#147
sammywinchester19
closed
3 years ago
1
marking duplicates
#146
olechnwin
opened
3 years ago
1
Can software assemble genomes at the chromosome level
#145
ld9866
closed
3 years ago
6
Restriction sites where the cut-site is in the middle.
#144
DustinSokolowski
closed
3 years ago
2
About plot in your article
#143
zhoudreames
closed
3 years ago
1
ImportError: No module named networkx
#142
khush876
closed
3 years ago
1
Omni-C
#141
ardy20
closed
3 years ago
1
KeyError:
#140
kalbflei
closed
3 years ago
2
fix bugs
#139
c-zhou
closed
3 years ago
0
Generating .hic file with convert.sh
#138
kishor2019
opened
3 years ago
4
Still runs with empty bed
#137
aakashsur
opened
3 years ago
0
Numpy Requirement
#136
aakashsur
closed
3 years ago
1
Proximo Hi-C (Phase Genomics)
#135
carolhsb
closed
3 years ago
3
sorting bed file
#134
kishor2019
closed
3 years ago
2
Two HiC experiments: recommend combine data or run SALSA sequentially?
#133
ckeeling
closed
1 year ago
2
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