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2
votes
1
answer
390
views
8 follow
1
answer
Comparing SPAdes assemblies to each other?
spades denovo written 20 months ago by laurenkleine18 • 20 • updated 5 days ago by Istvan Albert ♦♦ 84k
0
votes
1
answer
137
views
1
answer
Generate single genome consensus fasta file from SPAdes output: viral genome sequencing
genome fasta spades viral genome assembly virus written 9 weeks ago by snow_seq • 0 • updated 9 weeks ago by Asaf ♦ 8.1k
0
votes
0
answers
137
views
0
answers
Determining reason for low quality assembly
assembly spades written 4 months ago by liorglic • 310
1
vote
2
answers
286
views
2
answers
Problem running QUAST assembly evaluation: quast tries to write to read-only FS
spades quast written 5 months ago by tospo • 50
0
votes
0
answers
188
views
0
answers
Problem with memory requirements for SPades
assembly spades written 5 months ago by Tospohh • 10
6
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2
answers
3.1k
views
2
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Where can i get library.txt file for SSPACE?
sspace spades written 4.0 years ago by Calvin • 60 • updated 6 months ago by Naomifu • 0
55
votes
4
answers
824
views
5 follow
4
answers
How to determine species of paired-end .fastq files (low mapping rates and inconsistent findings)
sendsketch spades bacteria kraken blast written 9 months ago by LRStar • 190 • updated 6 months ago by jbnrodriguez • 0
2
votes
0
answers
285
views
0
answers
Prokka and plasmidspades unexpectedly reveal no plasmid
plasmid spades prokka plasmidspades written 8 months ago by claping • 0
0
votes
0
answers
262
views
0
answers
Spades has been running for over a week. Normal?
genome assembly spades written 8 months ago by stacy734 • 40
5
votes
1
answer
699
views
1
answer
How to run spades.py for multiple files(fastq) at once?
assembly loop sequence fastq spades written 10 months ago by subrahmanya • 0
4
votes
1
answer
364
views
1
answer
Assemble bacterial .fastq files and find differences (SPAdes followed by MUMmer)
spades mummer bacteria contig snp written 10 months ago by LRStar • 190 • updated 10 months ago by Joe ♦ 17k
0
votes
0
answers
220
views
0
answers
Run Ray Assembler with multiple kmer values
genome assembly ray spades gene written 10 months ago by gustavojorge080 • 0
0
votes
1
answer
278
views
1
answer
what is Kmer coverage
genome assembly sequence metagenome spades written 10 months ago by vm.higareda • 20 • updated 10 months ago by Buffo • 1.8k
0
votes
0
answers
216
views
0
answers
Does SPAdes assembler lose singlets?
assembly spades genomes written 10 months ago by stacy734 • 40
3
votes
1
answer
688
views
1
answer
SPAdes error during assembly, error code -6
software error assembly spades written 11 months ago by marongiu.luigi • 520 • updated 11 months ago by h.mon ♦ 30k
0
votes
0
answers
467
views
0
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SPAdes error code -6
assembly metagenomics spades written 12 months ago by Lina F • 160
3
votes
1
answer
1.2k
views
1
answer
Should I consider contigs.fa or scaffolds.fa from SPAdes output for downstream analyses?
assembly spades quast contigs written 13 months ago by bioinforesearchquestions • 280 • updated 13 months ago by h.mon ♦ 30k
5
votes
1
answer
653
views
1
answer
Kmer selection for bacterial WGS denovo assembly using SPAdes or SOAP-denovo
wgs assembly spades soap-denovo bacterial written 13 months ago by bioinforesearchquestions • 280 • updated 13 months ago by h.mon ♦ 30k
0
votes
0
answers
405
views
0
answers
Assembly finished but output contig file is empty
assembly spades sequencing written 14 months ago by tchow5 • 0
0
votes
0
answers
586
views
0
answers
Different metrics with same kmer values in SPAdes assembly
assembly spades kmer written 14 months ago by gustavo.teixeira • 0 • updated 14 months ago by ATpoint ♦ 36k
9
votes
3
answers
4.0k
views
8 follow
3
answers
Criteria for filtering contigs after spades assembly
assembly spades contigs filtering written 2.5 years ago by fhsantanna • 490 • updated 16 months ago by bhclement • 0
4
votes
1
answer
987
views
1
answer
Increase memory limit in SPAdes-3.6.1
hybrid assembly next-gen alignment spades written 16 months ago by ashaneev07 • 20 • updated 16 months ago by Buffo • 1.8k
5
votes
1
answer
1.2k
views
1
answer
How to give merged reads as input in spades
merged assembly spades de novo written 18 months ago by manjumoorthy95 • 20 • updated 18 months ago by Joseph Hughes • 2.8k
2
votes
0
answers
680
views
0
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Differences in annotations using Prokka on assembly done by SPAdes
annotation spades prokka written 20 months ago by jeetsahu • 10 • updated 18 months ago by Biostar ♦♦ 20
0
votes
0
answers
570
views
0
answers
SPAdes stuck for almost 24h, restart it didn't work
spades written 18 months ago by lucia • 10 • updated 18 months ago by Joe ♦ 17k
0
votes
0
answers
819
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0
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How to get a consensus of the contigs obtained from an assembler like spades?
consensus spades contigs written 19 months ago by DanielC • 120
8
votes
1
answer
1.3k
views
6 follow
1
answer
looping a list of trimed fasta files to run spades assembler
assembly loop sequence loop a list spades written 20 months ago by m.al_amiri • 20
13
votes
3
answers
6.5k
views
5 follow
3
answers
How do I access genome coverage using SPADES?
genome spades coverage myposts written 4.9 years ago by fhsantanna • 490 • updated 20 months ago by DanielC • 120
3
votes
1
answer
665
views
1
answer
Perl script review
perl spades written 20 months ago by Mostafa Mahmoud • 0 • updated 20 months ago by Michael Dondrup ♦ 47k
5
votes
0
answers
1.6k
views
0
answers
SPAdes output with assembling warning
sequence-reads spades assembling iontorrent written 21 months ago by DanielC • 120
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