tag:blogger.com,1999:blog-1071661434473559589.post7862821123611122573..comments2024-03-19T13:22:17.079+11:00Comments on The Genome Factory: Using Velvet with mate-pair sequencesTorsten Seemannhttp://www.blogger.com/profile/12241185247897084810noreply@blogger.comBlogger47125tag:blogger.com,1999:blog-1071661434473559589.post-47194786647291749162022-08-28T21:16:22.018+10:002022-08-28T21:16:22.018+10:00Hi Admin, I hope are fine. I'm your one of the...Hi Admin, I hope are fine. I'm your one of the biggest fans, I like to read your blogs and I've also shared your blogs with my family members and friends. I hope in future you'll publish more blogs like your old ones. Please accept my thanks on my behalf of me and from my family and friends.<br /><br /><br /><a href="https://1947housingislamabad.pk" rel="nofollow">1947 Housing Islamabad</a><br /><a href="https://www.smartprojectsislamabad.com/2020/03/22/capital-smart-city/" rel="nofollow">Capital Smart City</a><br /><a href="https://www.smartprojectsislamabad.com/lahore-smart-city/" rel="nofollow">Lahore Smart City</a><br /><a href="https://www.smartprojectsislamabad.com/new-metro-city-gujar-khan" rel="nofollow">New Metro City Gujar Khan</a><br /><a href="https://hottubhire-skiphirenear.com" rel="nofollow">Skip Hire Near Me</a><br /><a href="http://1947housingislamabad.pk" rel="nofollow">1947 Housing Islamabad</a>Lynne Allenhttps://www.blogger.com/profile/18104010002188937732noreply@blogger.comtag:blogger.com,1999:blog-1071661434473559589.post-70813282716131535792021-08-11T22:30:50.190+10:002021-08-11T22:30:50.190+10:00All thanks to Dr OLIHA for curing my herpes virus/...All thanks to Dr OLIHA for curing my herpes virus/hpv with his herbal medicine, i do not have much to say but with all my life i will forever be grateful to him and God Almighty for using Dr OLIHA to reach me when i thought it was all over, today i am happy with my life again after the medical doctor have confirmed my HERPES SIMPLEX VIRUS / HPV of 5 is gone,i have never in my life believed that HERPES SIMPLEX VIRUS could be cured by herbal medicine. so i want to use this means to reach other persons who have this disease by testifying the power of Dr OLIHA that all hope is not lost yet, try and contact him by any means for any kind of disease with his email: oliha.miraclemedicine@gmail.com add him on whatsapp line or call +2349038382931.Alexis Gracehttps://www.blogger.com/profile/16131289852530459964noreply@blogger.comtag:blogger.com,1999:blog-1071661434473559589.post-3197730450766362832020-04-15T08:36:44.891+10:002020-04-15T08:36:44.891+10:00It depends on which mate pair protocol and adaptor...It depends on which mate pair protocol and adaptors you used. Look at `nxtrim`.Torsten Seemannhttps://www.blogger.com/profile/12241185247897084810noreply@blogger.comtag:blogger.com,1999:blog-1071661434473559589.post-11083987128617826072020-04-15T00:43:52.595+10:002020-04-15T00:43:52.595+10:00Could you provide a removal adapter for Mate pair ...Could you provide a removal adapter for Mate pair library before use velvet<br /><br />Thanks!AmarĂahttps://www.blogger.com/profile/10567985526617989781noreply@blogger.comtag:blogger.com,1999:blog-1071661434473559589.post-84560394489248329522016-10-25T09:02:56.336+11:002016-10-25T09:02:56.336+11:00De novo genome assembly would be easy if there wer...De novo genome assembly would be easy if there were no repeats in the genome, and no errors in the reads. We can improve error rate with better technology, but we can never change the genomes. Repeats produce ambiguous hubs in the assembly graph. The only way to untangle a repeat of length L is to have reads, or "read spans" that are LONGER than L bp. That's why Mate Pair reads are used, as they span up to 40 kbp of the genome, wherease Paired End reads only reach ~600bp.<br /><br /><br /><br />You might like to read some of the slides I have given on this topic:<br />http://www.slideshare.net/torstenseemann/presentationsTorsten Seemannhttps://www.blogger.com/profile/12241185247897084810noreply@blogger.comtag:blogger.com,1999:blog-1071661434473559589.post-81811491644696208782016-10-24T22:54:27.611+11:002016-10-24T22:54:27.611+11:00Hello Torsten,
You are really doin...Hello Torsten,<br /> You are really doing a wonderful work by writing here . It really helps the beginners in de novo assembly.Here, i have one question that why all 3 libraries (SE reads, PE reads and Mate PE reads) of an organism should be combined and assembled? Combining 3 libraries will improve the assembly quality? could you answer me this?saravanan selvamhttps://www.blogger.com/profile/07167775730098820396noreply@blogger.comtag:blogger.com,1999:blog-1071661434473559589.post-3555129876090440472016-03-23T11:05:46.930+11:002016-03-23T11:05:46.930+11:00This comment has been removed by the author.Anonymoushttps://www.blogger.com/profile/17309944221528065621noreply@blogger.comtag:blogger.com,1999:blog-1071661434473559589.post-45963472790017687972016-03-23T10:38:56.454+11:002016-03-23T10:38:56.454+11:00I am using velvet to assemble fungal genome (~30 m...I am using velvet to assemble fungal genome (~30 million reads). I have compiled velvet with 'MAXKMERLENGTH=165' and 'openmp=1' to handle my 150bp reads. I am getting memory error ( velveth: Can't malloc 207 chars: Cannot allocate memory). Below is my script that shows the memory I requested. <br /><br />#PBS -q standard<br />#PBS -l jobtype=cluster_only <br /><br />### Set the number of cpus that will be used.<br />#PBS -l select=1:ncpus=4:mem=8Gb:pcmem=4gb<br />#PBS -l pvmem=4gb<br />#PBS -l cput=30:0:0<br />#PBS -l walltime=24:0:0<br /><br />source /usr/share/Modules/init/bash<br /><br />module load unsupported<br />module load nirav/velvet/1.2.10<br /><br />#Get things ready to use threaded (OMP) version of Velvet<br />#Set OMP_THREAD_LIMIT--will be the same as ppn above<br />export OMP_THREAD_LIMIT=4<br /> <br />#Set OMP_NUM_THREADS--will be 1 lower than ppn <br />NUM_THREADS=3<br />export OMP_NUM_THREADS=$NUM_THREADS<br /> <br /># Write something to record what thread limits were used. <br />echo Limiting Velvet to $PBS_NP threads total with $NUM_THREADS slave threads.<br /><br />cd $PBS_O_WORKDIR/1st_assembly<br /><br />velveth fungal 125,155,10 -fastq.gz -shortPaired -separate /rsgrps2/sjmiller/Illumina_JeeHan/160224_M03132_0042_000000000-ALYFG_Analysis_fastq_files/Parasite_S1_L001_R1_001.fastq.gz \<br />/rsgrps2/sjmiller/Illumina_JeeHan/160224_M03132_0042_000000000-ALYFG_Analysis_fastq_files/Parasite_S1_L001_R1_001.fastq.gz<br /><br />I know I am requesting way too less memory but my question is what is appropriate memory that could handle my dataset?<br /><br />Thanks,<br />M<br /> Anonymoushttps://www.blogger.com/profile/17309944221528065621noreply@blogger.comtag:blogger.com,1999:blog-1071661434473559589.post-53264804678237270942015-12-15T14:53:12.560+11:002015-12-15T14:53:12.560+11:00Hi Torsten,
recently i was trying to assemble my g...Hi Torsten,<br />recently i was trying to assemble my genome with 3 libraries,and how to determin the -ins_length option if i want to assemble with all the libraries? Is it necessary ao add this option to improve my assembly results? if i assemble with separate library ,how could i combine these results into one ?<br />Looking forward to your replysonghttps://www.blogger.com/profile/16156082662538378276noreply@blogger.comtag:blogger.com,1999:blog-1071661434473559589.post-63342787197901757182015-11-24T17:21:39.861+11:002015-11-24T17:21:39.861+11:00Hi Torsten,
I started to do velvet recently, i wa...Hi Torsten,<br /><br />I started to do velvet recently, i want to know all the basic things about Velvet. i hate the official manual which one is i downloaded from the Velevt official page. Could you pls sugeest me any of the Articles and Velvet manual...<br /><br />Best,<br /><br />K.Kathir#IamKathir#InSearchingOfLifehttps://www.blogger.com/profile/17604199654590105625noreply@blogger.comtag:blogger.com,1999:blog-1071661434473559589.post-75530862540884845112015-11-01T08:34:50.113+11:002015-11-01T08:34:50.113+11:00Most modern assemblers no longer use a single k-me...Most modern assemblers no longer use a single k-mer value. They combine assemblies of multiple k-mer values.<br /><br />You may want to assemble just the PE reads first into contigs, then use an external scaffolder to use the MP reads to join and order contigs.<br />Torsten Seemannhttps://www.blogger.com/profile/12241185247897084810noreply@blogger.comtag:blogger.com,1999:blog-1071661434473559589.post-58384650710268419182015-10-31T22:30:03.738+11:002015-10-31T22:30:03.738+11:00Hi Torsten,
I was wondering how using PE and MP re...Hi Torsten,<br />I was wondering how using PE and MP reads of different lengths would affect the best k-mer size? If you have, say, a best k-mer size for the PE reads that is longer than the MP read length.<br /><br /> dryashttps://www.blogger.com/profile/10563877517033082983noreply@blogger.comtag:blogger.com,1999:blog-1071661434473559589.post-81582802905632342402015-09-30T17:09:25.153+10:002015-09-30T17:09:25.153+10:00Ok, thanks a lot!Ok, thanks a lot!Anonymoushttps://www.blogger.com/profile/09800321448020130149noreply@blogger.comtag:blogger.com,1999:blog-1071661434473559589.post-37483184736005114662015-09-30T08:25:59.543+10:002015-09-30T08:25:59.543+10:00Trim the reads first, then correct the reads, then...Trim the reads first, then correct the reads, then reverse complement for the assembler last.Torsten Seemannhttps://www.blogger.com/profile/12241185247897084810noreply@blogger.comtag:blogger.com,1999:blog-1071661434473559589.post-89567780709471386872015-09-29T19:32:22.095+10:002015-09-29T19:32:22.095+10:00Hi Torsten,
Thanks for the this informative post. ...Hi Torsten,<br />Thanks for the this informative post. <br />I now using hybrid data of pair-end and mate-pair reads to assemble. I want to perform error correct before assemble. Should I reverse complement the mate-pair reads before I correct the error for all of my data. Or can I correct them and then reverse complement the mate-pair data before assemble?Anonymoushttps://www.blogger.com/profile/09800321448020130149noreply@blogger.comtag:blogger.com,1999:blog-1071661434473559589.post-12578230663981094582014-08-01T06:23:27.474+10:002014-08-01T06:23:27.474+10:00Thank you for the reply.
I have used Meta-Velvet h...Thank you for the reply.<br />I have used Meta-Velvet here at the last step, but the results or the contigs which are produced after it and after velvetg are same in number.<br /><br />I tried the same approach with Miseq data but it looked same.<br />I will try Ray-Meta.<br /><br />Thanks!bioinfohttps://www.blogger.com/profile/11273465319290797420noreply@blogger.comtag:blogger.com,1999:blog-1071661434473559589.post-70896098057305667252014-08-01T06:14:21.967+10:002014-08-01T06:14:21.967+10:00Your result is not surprising. Velvet is not well ...Your result is not surprising. Velvet is not well suited to Proton data, it works best with Illumina. Also Velvet is not designed for meta-genomes, which have a mixture of species of different coverages. <br /><br />You should consider a more specific tool, eg. Meta-Velvet or Ray-Meta. The Khmer project also has a protocol for assembling meta-genomes: https://khmer-protocols.readthedocs.org/en/latest/metagenomics/<br /><br />Torsten Seemannhttps://www.blogger.com/profile/12241185247897084810noreply@blogger.comtag:blogger.com,1999:blog-1071661434473559589.post-31779546901054159962014-08-01T06:05:33.180+10:002014-08-01T06:05:33.180+10:00Hi Torsten,
Thank you for such an informative p...Hi Torsten,<br /> Thank you for such an informative post. <br /> I am using metavelvet to assemble metagenome generated by Ion Proton, there sre 23 million SE reads.<br />I have used the following commands:<br />velveth runAll_a/ 21 -short ionExpress_nofilter.fasta<br /><br />velvetg runAll_a/ -exp_cov auto<br /><br />meta-velvetg runAll_a/<br /><br />The last line of the output is:<br /><br />Final graph has 4272026 nodes and n50 of 101, max 1932, total 178452348, using 19006699/23565054 reads<br /><br />I am confused or rather surprised with this line. Isn't the contigs are too many. <br />Also, when I ran the python script "scriptEstimatedCovMulti.py" I am getting peak as[-1] and I am not sure what that is.<br />The coverage is also very low.<br /> I would like to know if the method I am adopting is correct or I need to modify some steps to get improved results.<br />I will be thankful if any one could help me figure out if I am on right track.<br /><br />Thanks!<br />bioinfohttps://www.blogger.com/profile/11273465319290797420noreply@blogger.comtag:blogger.com,1999:blog-1071661434473559589.post-59860767527652067122014-05-20T06:17:12.989+10:002014-05-20T06:17:12.989+10:00Hi Torsten,
Thanks for the this informative post. ...Hi Torsten,<br />Thanks for the this informative post. Do you know any tool designed to trim (and reverse the reads if necessary) for adapters specifically for illumina mate-pair libraries ? Based on the junction adapter(s) present in the read MPs might have different orientation so reversing all the reads seems not the best option. I could write my own code for this but I wanted to check first to see if there is anything available. <br /><br />Thanks<br />Hamdi Hamdi Kitapcihttps://www.blogger.com/profile/04450447737495524495noreply@blogger.comtag:blogger.com,1999:blog-1071661434473559589.post-47128445923147686522014-05-09T09:26:56.528+10:002014-05-09T09:26:56.528+10:00As per manual: make 'CATEGORIES=57' (in th...As per manual: make 'CATEGORIES=57' (in the unlikely event you have 57 separate libraries to assemble)Danhttps://www.blogger.com/profile/13016862723677027934noreply@blogger.comtag:blogger.com,1999:blog-1071661434473559589.post-82279797348479544302014-05-09T09:22:35.552+10:002014-05-09T09:22:35.552+10:00Hi Torsten, great post. One thing I'd point ou...Hi Torsten, great post. One thing I'd point out is that Velvet does not compile with 3 categories (for 3 libraries) by default (it defaults to 2) so to use more than 2 libraries in an assembly, you need to compile velvet with the CATEGORIES option.Danhttps://www.blogger.com/profile/13016862723677027934noreply@blogger.comtag:blogger.com,1999:blog-1071661434473559589.post-22846280629504745322013-10-16T21:06:43.497+11:002013-10-16T21:06:43.497+11:00In which version there is the possibility of using...In which version there is the possibility of using the -separate option for paired-ends reads? in Version 1.2.03 I get an unknown option error for that.Matteo Brillihttps://www.blogger.com/profile/00038562628438681682noreply@blogger.comtag:blogger.com,1999:blog-1071661434473559589.post-40731648923990385992013-08-09T09:11:46.571+10:002013-08-09T09:11:46.571+10:00Thanks, agreed - CheersThanks, agreed - CheersDave Wheelerhttps://www.blogger.com/profile/11796791305932226696noreply@blogger.comtag:blogger.com,1999:blog-1071661434473559589.post-24953055416827267592013-08-08T16:03:41.463+10:002013-08-08T16:03:41.463+10:00You are right that the probability of erroneous K-...You are right that the probability of erroneous K-mers does increase with K. You can only increase K if you also increase your read coverage too, so that we get enough correct K-mers (signal) to counteract the false K-mers (noise). Read clipping and read correction are often used to drastically reduce the number of false K-mers being put into the graph, which reduces memory usage and improves graph simplification. <br /><br />For bacteria we usually have lots of coverage, sometimes > 1000x so using higher K-mers improves the assembly in practice. The error rate of Illumina is well below 1% now, so false K-mers are less likely than one might first expect (after clipping). Some studies have shown that K=24 is "mostly unique" in genomes, but mostly doesn't make them all unique.<br /><br />Thanks for taking the time to comment.<br /><br />Torst<br />Torsten Seemannhttps://www.blogger.com/profile/12241185247897084810noreply@blogger.comtag:blogger.com,1999:blog-1071661434473559589.post-6324333721780240532013-08-08T11:56:57.919+10:002013-08-08T11:56:57.919+10:00Just the info I was after - thanks!
With regard t...Just the info I was after - thanks!<br /><br />With regard to the question about longer kmer values though (ie ~100), won't the increased probability of encountering a sequencing error start to create problems in the assembly. There will also be less overlaps that fit into this big kmer value. With the exception of long repeats, I would have thought inappropriate overlaps greater than 50 bp would be rare, so not much is gained anyway. Hope that makes sense!Dave Wheelerhttps://www.blogger.com/profile/11796791305932226696noreply@blogger.com