c-zhou / yahs

Yet another Hi-C scaffolding tool

c-zhou/yahs Issues

There is no longer a need to manually set the scale factor in Juicebox
Updated a month ago15
trouble generating HiC contact map
Closed 2 months ago1
YAHS merges two chromosomes in alternate haplotype
Updated 3 months ago7
specifying restriction enzyme cutting sites with -e
Closed 3 months ago2
Hi-C Assembly Results Identical to HiFi Assembly, No Notable Improvement
Closed 3 months ago
0 read pairs
Updated 3 months ago21
No reads in Hi-C contact matrices.
Updated 4 months ago10
yahs result output bin file is faulty
Closed 4 months ago1
The bin file error
Closed 4 months ago
Unexpected Zero Reads Pairs and Output Size with yahs and Juicer Preprocessing Pipeline
Updated 4 months ago4
yahs can't read PA5 file format file
Closed a year ago
No intra links and inter links dumped from bam file
Closed 5 months ago3
Juicer files only allow manual curation of first scaffold in JBAT
Updated 5 months ago2
Scaffolding by yahs introduces 200 bp gaps in the assembly
Updated 5 months ago3
How you ever seen a hic heatmap like this one?
Updated 5 months ago2
stack smashing detected
Updated 7 months ago1
juicer_pre for edited scaffolds
Closed 7 months ago
Assembly metrics have gotten worse than hifiasm-only assembly
Updated 7 months ago5
generate hic contact map based on purged genome?
Updated 7 months ago3
The question about regenerating a HiC contact map for the final assembly
Updated 8 months ago
Difference between v1.2 and v1.2a.1?
Updated 8 months ago10
No inter links from bed file?
Updated 8 months ago11
Combining PoreC data
Updated 8 months ago1
YAHS output is identical to the input assembly
Updated 9 months ago3
juicer_tools pre runs for days then encounters java.lang.NullPointerException
Updated 10 months ago14
Round of yahs
Updated 10 months ago1
hic interactions statistics
Updated 10 months ago3
chromosome number more tnan my species
Updated a year ago2
two short(1000bp) contigs are generated by YaHS
Updated a year ago1
error occurred after setting the "yahs -l" parameter
Updated a year ago1
Using Yahs only to break contigs
Closed a year ago2
Segmentation fault (core dumped)
Updated a year ago1
Empty alignments_sorted.txt
Updated a year ago9
Are there any requirements for the input genome assembly results?
Closed a year ago2
After manual correction of juicebox convert agp to fasta
Updated a year ago1
How to display all hic signals
Updated a year ago1
Looking for suggesion on rerunning Yahs multiple rounds
Updated a year ago
Why is the proportion of sequences anchored to chromosomes low?
Updated a year ago
Breaking contigs to scaffold ?
Updated a year ago
Help needed to install yahs package (make failed)
Updated a year ago1
Contact map for unscaffolded assembly
Updated a year ago1
question about agp type N GAP_SZ 200
Updated a year ago3
Aborted (core dumped)
Updated 2 years ago4
segmentation fault during juicer pro
Updated 2 years ago
parameter for fixing assembly error
Updated 2 years ago
Same dataset works as .bam file but not .bed file
Updated 2 years ago5
manual editing with juicer pre creating an empty bed format out_JBAT.txt file
Closed 2 years ago2
Scaling issues for large genomes on juicebox
Closed 2 years ago6
'juicer pre' causes genome size changes
Closed 2 years ago1
Sex chromosomes
Updated 2 years ago1