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BGI-SOAP
1–17 of 460
Welcome to
BGI-SOAP
group. The
SOAP
website is
http://soap.genomics.org.cn/
And welcome any question about :
SOAP/SOAP3/SOAPaligner, SOAPdenovo, SOAPindel, SOAPsnv, SOAPsv, SOAPfusion, SOAPfuse, SOAPslice, SOAPsnp
general stuff about Bioinformatics, Genomics, Sequencing , NGS , GWAS
sequence alignment, assembly , analysis, visualization
RULES:
Be nice !
Learn, share and help each other.
This is an open community - not an additional service or support from BGI , so DO NOT request service or product or publish business information.
The last one, the very common one - How to ask question ?
How to ask question - the smart way:
http://www.catb.org/~esr/
faqs/smart-questions.html
How to ask question intelligently :
http://www.wikihow.com/Ask-a-
Question-Intelligently
Netiquette Guidelines :
http://www.ietf.org/rfc/
rfc1855.txt
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Ferdi
5/13/13
Too few PE links
Hi - I'm assembling an invertebrate genome of ~500Mb using SOAPdenovo2. For the scaffolding, I
unread,
SOAPdenovo
Too few PE links
Hi - I'm assembling an invertebrate genome of ~500Mb using SOAPdenovo2. For the scaffolding, I
5/13/13
Kim
,
黄伟华
2
5/7/13
Pregraph and contig modules work, but not map and scaff
The rd_len_cutoff in the config file should be set to the length of read(eg 100). Weihua Huang BGI
unread,
SOAPdenovo
Pregraph and contig modules work, but not map and scaff
The rd_len_cutoff in the config file should be set to the length of read(eg 100). Weihua Huang BGI
5/7/13
fyusufi
, …
谢寅龙(Long Xie)
16
3/10/17
Segmentation fault in SOAPdenovo multi-kmer
The github I sent you before was the latest version v1.04. Best, Yinlong Xie MGI From: bgi-soap@
unread,
SOAPdenovo
Segmentation fault in SOAPdenovo multi-kmer
The github I sent you before was the latest version v1.04. Best, Yinlong Xie MGI From: bgi-soap@
3/10/17
wsg
, …
Topulaneus Hattum
5
3/11/14
SOAPdenovo and paired end or unpaired FASTA files
It appears Tablet places some asterisks as place-holders in some of the sequences I was checking.
unread,
SOAPdenovo
SOAPdenovo and paired end or unpaired FASTA files
It appears Tablet places some asterisks as place-holders in some of the sequences I was checking.
3/11/14
Yifang Tan
3/19/13
Q&A
What does "PE links 0" or "Too few PE links" mean?
Hello, I was trying SOAPdenovo2, but could not get any meaningful contig (max contig length is only
unread,
SOAPdenovo
Q&A
What does "PE links 0" or "Too few PE links" mean?
Hello, I was trying SOAPdenovo2, but could not get any meaningful contig (max contig length is only
3/19/13
mor rubinstein
3/12/13
KmerFreqCutoff still leaves kmers of cover 1
Dear all, Please help me as I found no reference to this topic in the discussions here or anywhere
unread,
SOAPdenovo
KmerFreqCutoff still leaves kmers of cover 1
Dear all, Please help me as I found no reference to this topic in the discussions here or anywhere
3/12/13
Yun-juan Chang
, …
Steven VB
4
5/20/14
Segmentation fault
Hi, could there be something wrong with the format of my fastq files? @FCC4BKEACXX:7:1101:1201:2157#
unread,
SOAPdenovo
Segmentation fault
Hi, could there be something wrong with the format of my fastq files? @FCC4BKEACXX:7:1101:1201:2157#
5/20/14
Yong Hui Yee
3/10/13
Is there any option to set minimum contig size in SOUPdenovo?
Dear all, I have ran SOUPdenovo for transcriptome assembly using reads generated by Illumina paired-
unread,
SOAPdenovo
Is there any option to set minimum contig size in SOUPdenovo?
Dear all, I have ran SOUPdenovo for transcriptome assembly using reads generated by Illumina paired-
3/10/13
Helene Fradin
,
Manoj Samanta
2
3/27/13
Q&A
Assembly of heterozygous genomes by SOPAdenovo2
I do not think SOAPdenovo2 algorithm can take care of polymorphic genomes well. You may take a look
unread,
SOAPdenovo
Q&A
Assembly of heterozygous genomes by SOPAdenovo2
I do not think SOAPdenovo2 algorithm can take care of polymorphic genomes well. You may take a look
3/27/13
Radhika Khetani
, …
Manoj Samanta
4
2/20/13
kmerFreq
Radhika, Please do not forget another possibility - too many duplicate reads. Manoj -- Manoj Pratim
unread,
SOAPdenovo
kmerFreq
Radhika, Please do not forget another possibility - too many duplicate reads. Manoj -- Manoj Pratim
2/20/13
sendru
, …
lizhenyu
9
3/1/13
help for soapdenovo2
You can make false PE-read files by treating the single end read as both read1 and read2 of PE-read.
unread,
SOAPdenovo
help for soapdenovo2
You can make false PE-read files by treating the single end read as both read1 and read2 of PE-read.
3/1/13
Rafik Neme
1/2/13
SOAPdenovo-Trans - Fork, Bubble, Linear, etc.
Hi, I just started using the transcriptome analysis tool and the output contains an extra piece of
unread,
SOAPdenovo
SOAPdenovo-Trans - Fork, Bubble, Linear, etc.
Hi, I just started using the transcriptome analysis tool and the output contains an extra piece of
1/2/13
Echo Chen
12/5/12
How to produce an agp file
Hi everyone, I wonder if there is a pipeline for building an agp file from SOAPdenovo outputs for
unread,
SOAPdenovo
How to produce an agp file
Hi everyone, I wonder if there is a pipeline for building an agp file from SOAPdenovo outputs for
12/5/12
sendru
11/29/12
Question regarding to the pipe-line of SOAPdenovo2
I am quite new for de novo assembly, and recently have some reads of mammal for analysis. The reads
unread,
SOAPdenovo
Question regarding to the pipe-line of SOAPdenovo2
I am quite new for de novo assembly, and recently have some reads of mammal for analysis. The reads
11/29/12
Marek Piatek
, …
李振宇
3
10/8/12
SOAPdenovo2 without '-u' -no average contig coverage reported
Hi Richard, SOAPdenovo will mask, or exclude as you said, contigs with very low and high coverage,
unread,
SOAPdenovo
SOAPdenovo2 without '-u' -no average contig coverage reported
Hi Richard, SOAPdenovo will mask, or exclude as you said, contigs with very low and high coverage,
10/8/12
David H
, …
luiscunhamx
8
8/29/13
Q&A
SOAPdenovo and colorspace reads
Dear Manoj, I just found this post, and I am having exactly the same problem, I have 3x different
unread,
SOAPdenovo
Q&A
SOAPdenovo and colorspace reads
Dear Manoj, I just found this post, and I am having exactly the same problem, I have 3x different
8/29/13
Richard Buggs
, …
李振宇
9
6/18/12
one PE library unused in scaffolding
aha, thanks! That would explain it! Richard On 18 Jun 2012, at 12:38, 李振宇 wrote: The q1 and q2 were
unread,
SOAPdenovo
one PE library unused in scaffolding
aha, thanks! That would explain it! Richard On 18 Jun 2012, at 12:38, 李振宇 wrote: The q1 and q2 were
6/18/12