# \#assembly **URL:** https://help.galaxyproject.org/tag/assembly/75.md [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) --- ## [instaGRAAL on usegalaxy.eu finishes as “ok” but all outputs are 0 bytes](https://help.galaxyproject.org/t/instagraal-on-usegalaxy-eu-finishes-as-ok-but-all-outputs-are-0-bytes/17733)
**Author:** [@alma.wis](https://help.galaxyproject.org/u/alma.wis)\ **Replies:** 5\ **Last updated:** [May 26, 2026, 6:00pm UTC](https://help.galaxyproject.org/t/instagraal-on-usegalaxy-eu-finishes-as-ok-but-all-outputs-are-0-bytes/17733 "2026-05-26T18:00:05Z")
Hi! I am reporting a likely problem with the instaGRAAL tool on usegalaxy.eu. I ran instaGRAAL (0.1.6+galaxy0) with these inputs: abs\_fragments\_contacts\_weighted.txt fragments\_list.txt info\_contigs.txt refe… --- ## [Error while running metaspades](https://help.galaxyproject.org/t/error-while-running-metaspades/9796)
**Author:** [@chi1989](https://help.galaxyproject.org/u/chi1989)\ **Replies:** 2\ **Last updated:** [April 18, 2026, 2:35am UTC](https://help.galaxyproject.org/t/error-while-running-metaspades/9796 "2026-04-18T02:35:14Z")
Hi all, I am running Metaspade on my genome data. I have got { “code\_desc”: “”, “desc”: “Fatal error: Exit code 120 ()”, “error\_level”: 3, “exit\_code”: 120, “type”: “exit\_code” } as my error message. What has gone wron… --- ## [Fatal error: using trinity](https://help.galaxyproject.org/t/fatal-error-using-trinity/10218)
**Author:** [@guser](https://help.galaxyproject.org/u/guser)\ **Replies:** 2\ **Last updated:** [April 18, 2026, 2:32am UTC](https://help.galaxyproject.org/t/fatal-error-using-trinity/10218 "2026-04-18T02:32:45Z")
Hi I am using trinity and the error message is: "Fatal error: Exit code 1 () cp: -r not specified; omitting directory ‘trinity\_out\_dir/Trinity.tmp.fasta.salmon.idx’ /ocean/projects/mcb140028p/xcgalaxy/main/staging/50… --- ## [Error with de novo assembly using Trintiy](https://help.galaxyproject.org/t/error-with-de-novo-assembly-using-trintiy/10563)
**Author:** [@Jose\_Manuel\_Latorre](https://help.galaxyproject.org/u/Jose_Manuel_Latorre)\ **Replies:** 5\ **Last updated:** [April 18, 2026, 2:28am UTC](https://help.galaxyproject.org/t/error-with-de-novo-assembly-using-trintiy/10563 "2026-04-18T02:28:46Z")
Dear Galaxy users, First, thanks in advance for your help, I am trying to get a de novo assembly from RNA-Seq data using Trintiy. I have just one sample that was sequenced in the Illumina platform with more or less 40 … --- ## [How to use MEGAHIT](https://help.galaxyproject.org/t/how-to-use-megahit/12155)
**Author:** [@MarwahSabo](https://help.galaxyproject.org/u/MarwahSabo)\ **Replies:** 2\ **Last updated:** [April 18, 2026, 1:59am UTC](https://help.galaxyproject.org/t/how-to-use-megahit/12155 "2026-04-18T01:59:25Z")
hallow I’m trying to assembly my data by megahit. it cannot run don’t know why anyone can helps. --- ## [SPAdes: why and how to use intact Paired End reads, plus production workflows for Bacterial assembly!](https://help.galaxyproject.org/t/spades-why-and-how-to-use-intact-paired-end-reads-plus-production-workflows-for-bacterial-assembly/17630)
**Author:** [@Michael\_Thon](https://help.galaxyproject.org/u/Michael_Thon)\ **Replies:** 1\ **Last updated:** [April 6, 2026, 6:21pm UTC](https://help.galaxyproject.org/t/spades-why-and-how-to-use-intact-paired-end-reads-plus-production-workflows-for-bacterial-assembly/17630 "2026-04-06T18:21:08Z")
Hi all - I’m using SPAdes to assemble a bacterial genome. When the paired reads are in a dataset of paired reads I get an error. When I enter them as single reads it seems to work fine. Maybe its a problem with my da… --- ## [Unequal contig length of haplotype assemblies?](https://help.galaxyproject.org/t/unequal-contig-length-of-haplotype-assemblies/16379)
**Author:** [@nirjana\_dewan](https://help.galaxyproject.org/u/nirjana_dewan)\ **Replies:** 3\ **Last updated:** [October 17, 2025, 8:27pm UTC](https://help.galaxyproject.org/t/unequal-contig-length-of-haplotype-assemblies/16379 "2025-10-17T20:27:56Z")
Hello! I am currently trying to put together an avian reference genome using the Vertebrate Genome Project workflow on Galaxy. To provide some context, I have HiC and HiFi sequences from the same individual (female spec… --- ## [Memory error with rnaSPAdes? Try QA/QC and Sub-sample sequences](https://help.galaxyproject.org/t/memory-error-with-rnaspades-try-qa-qc-and-sub-sample-sequences/16326)
**Author:** [@vishal\_jha](https://help.galaxyproject.org/u/vishal_jha)\ **Replies:** 1\ **Last updated:** [September 30, 2025, 5:52pm UTC](https://help.galaxyproject.org/t/memory-error-with-rnaspades-try-qa-qc-and-sub-sample-sequences/16326 "2025-09-30T17:52:15Z")
I am facing issue with rnaspades, it is not working for some of the data while format of all the data that I am using is corect --- ## [Assembly: species specific coverage questions? See VPG resources!](https://help.galaxyproject.org/t/assembly-species-specific-coverage-questions-see-vpg-resources/16268)
**Author:** [@Derek\_Wilkinson](https://help.galaxyproject.org/u/Derek_Wilkinson)\ **Replies:** 1\ **Last updated:** [September 23, 2025, 8:41pm UTC](https://help.galaxyproject.org/t/assembly-species-specific-coverage-questions-see-vpg-resources/16268 "2025-09-23T20:41:22Z")
I used Galaxy Europe server and tool: Raven De novo assembly of Oxford Nanopore Technologies data (Galaxy version 1.8.3+Galaxy0 on a concatenated fastq file of ONT long reads. We have sequenced the fungus, Osmozyma mogii… --- ## [What are the different types of assembly?](https://help.galaxyproject.org/t/what-are-the-different-types-of-assembly/16269)
**Author:** [@Jon\_Colman](https://help.galaxyproject.org/u/Jon_Colman)\ **Replies:** 1\ **Last updated:** [September 23, 2025, 7:45pm UTC](https://help.galaxyproject.org/t/what-are-the-different-types-of-assembly/16269 "2025-09-23T19:45:44Z")
What programs are available for assembly of genome to reference using mapped reads??? --- ## [Flye giving error with bacterial genome](https://help.galaxyproject.org/t/flye-giving-error-with-bacterial-genome/16203)
**Author:** [@lcn](https://help.galaxyproject.org/u/lcn)\ **Replies:** 1\ **Last updated:** [August 21, 2025, 4:33pm UTC](https://help.galaxyproject.org/t/flye-giving-error-with-bacterial-genome/16203 "2025-08-21T16:33:17Z")
Hello community, I was trying to assemble a bacterial genome of about 2.1 Mb using flye. These are long reads produced with nanopore that I decompressed and then filtered by length; I have used this protocol several ti… --- ## [Large genome assembly? See VGP resources and access your self-serve extended data storage!](https://help.galaxyproject.org/t/large-genome-assembly-see-vgp-resources-and-access-your-self-serve-extended-data-storage/16194)
**Author:** [@Mokammel\_Hossain](https://help.galaxyproject.org/u/Mokammel_Hossain)\ **Replies:** 1\ **Last updated:** [August 20, 2025, 5:07pm UTC](https://help.galaxyproject.org/t/large-genome-assembly-see-vgp-resources-and-access-your-self-serve-extended-data-storage/16194 "2025-08-20T17:07:30Z")
After doing illumina sequencing, I have found forward (121.5 gb) and reverse (121.5 gb) fastq files of Fasciola gigantica. I want to do assembly using galaxy. Is it possible for this large size data? If yes, please tell … --- ## [Metaspades Single Reads](https://help.galaxyproject.org/t/metaspades-single-reads/15815)
**Author:** [@Jon\_Colman](https://help.galaxyproject.org/u/Jon_Colman)\ **Replies:** 5\ **Last updated:** [July 25, 2025, 8:34pm UTC](https://help.galaxyproject.org/t/metaspades-single-reads/15815 "2025-07-25T20:34:04Z")
When using interlaced reads for Metaspades, can I add Single unpaired reads to the end of the interlaced reads??? --- ## [nextdenovo empty fasta files](https://help.galaxyproject.org/t/nextdenovo-empty-fasta-files/11203)
**Author:** [@hogandj](https://help.galaxyproject.org/u/hogandj)\ **Replies:** 2\ **Last updated:** [June 25, 2025, 4:37am UTC](https://help.galaxyproject.org/t/nextdenovo-empty-fasta-files/11203 "2025-06-25T04:37:32Z")
Hi, I recently ran nextdenovo and while the run was “successful” and produced assembly stats and a configuration file, the fasta files were empty. There seems to be an error writing the file: here is the error log: \[220… --- ## [VGP - Workflow 1: K-mer Profiling - Need 2 PacBio Hifi Files But I Only Have 1](https://help.galaxyproject.org/t/vgp-workflow-1-k-mer-profiling-need-2-pacbio-hifi-files-but-i-only-have-1/15280)
**Author:** [@adswann](https://help.galaxyproject.org/u/adswann)\ **Replies:** 3\ **Last updated:** [April 23, 2025, 4:44pm UTC](https://help.galaxyproject.org/t/vgp-workflow-1-k-mer-profiling-need-2-pacbio-hifi-files-but-i-only-have-1/15280 "2025-04-23T16:44:10Z")
Hello! I’m an undergrad student, so please excuse me if there is a simple solution to this I’m not seeing. I’m trying to run the first workflow–K-mer profiling–in the VGP-Galaxy Assembly Workflows Series by following t… --- ## [Why to consider Shovill instead of SPADes](https://help.galaxyproject.org/t/why-to-consider-shovill-instead-of-spades/14863)
**Author:** [@Jennifer\_Kerr](https://help.galaxyproject.org/u/Jennifer_Kerr)\ **Replies:** 4\ **Last updated:** [March 1, 2025, 12:56am UTC](https://help.galaxyproject.org/t/why-to-consider-shovill-instead-of-spades/14863 "2025-03-01T00:56:12Z")
history: https://usegalaxy.org/u/jkerr/h/srr26975044-illumina-c-elegans-spain I tried running a workflow with shovil and shovil alone. Both showed a fatal error with illumina dataset from SRA download --- ## [Cheatsheet: How to combine Spades Operation Mode and Pipeline options](https://help.galaxyproject.org/t/cheatsheet-how-to-combine-spades-operation-mode-and-pipeline-options/14660)
**Author:** [@davide\_bersanetti](https://help.galaxyproject.org/u/davide_bersanetti)\ **Replies:** 4\ **Last updated:** [February 11, 2025, 5:56pm UTC](https://help.galaxyproject.org/t/cheatsheet-how-to-combine-spades-operation-mode-and-pipeline-options/14660 "2025-02-11T17:56:51Z")
Hi everyone! I am trying to run SPAdes on galaxy.eu , I have uploaded my paired ends ( after trimming) and specificed my work conditions. But the assembly is stopped by the following error " No assembly mode was specifie… --- ## [Breseq fastq format troubleshooting](https://help.galaxyproject.org/t/breseq-fastq-format-troubleshooting/14670)
**Author:** [@davide\_bersanetti](https://help.galaxyproject.org/u/davide_bersanetti)\ **Replies:** 3\ **Last updated:** [February 8, 2025, 11:19am UTC](https://help.galaxyproject.org/t/breseq-fastq-format-troubleshooting/14670 "2025-02-08T11:19:42Z")
Hi everyone I am trying to run Breseq but I keep getting the error shown in the image, no matter what type of data I use ( raw reads, trimmed, assemblies) What could be the reason? Thank you for any kind of help --- ## [Long read genome assemby](https://help.galaxyproject.org/t/long-read-genome-assemby/14146)
**Author:** [@HGM](https://help.galaxyproject.org/u/HGM)\ **Replies:** 1\ **Last updated:** [December 13, 2024, 10:12pm UTC](https://help.galaxyproject.org/t/long-read-genome-assemby/14146 "2024-12-13T22:12:00Z")
I did I tried to run a workflow to do a bacterial genome assembly of ONT sequences on Galaxy. I did initial raw sequences QC with FastQC and Nanoplot then trimmed using porechop I then went on to assemly with flye. I su… --- ## [How to analyze trimmed reads by Shovill Faster Spades Assembly tool](https://help.galaxyproject.org/t/how-to-analyze-trimmed-reads-by-shovill-faster-spades-assembly-tool/13790)
**Author:** [@huiping](https://help.galaxyproject.org/u/huiping)\ **Replies:** 2\ **Last updated:** [October 31, 2024, 8:31am UTC](https://help.galaxyproject.org/t/how-to-analyze-trimmed-reads-by-shovill-faster-spades-assembly-tool/13790 "2024-10-31T08:31:32Z")
Hi, I used your Timmomatic tool to trim my reads and obtained 4 files: fastq R1 paired, fastq R2 paired, fastq R1 unpaired and fastq R2 unpaired. Can I use Collapse Collection tool to get a single dataset, then use Shovi… --- ## [Aligner for Circular genomes](https://help.galaxyproject.org/t/aligner-for-circular-genomes/13746)
**Author:** [@Serkan\_ONDER](https://help.galaxyproject.org/u/Serkan_ONDER)\ **Replies:** 1\ **Last updated:** [October 23, 2024, 7:02am UTC](https://help.galaxyproject.org/t/aligner-for-circular-genomes/13746 "2024-10-23T07:02:19Z")
Does Galaxy has any aligner for Circular genomes? If you suggest one I will be glad. --- ## [How to make fasta file in a single sequence read like a reference genome?](https://help.galaxyproject.org/t/how-to-make-fasta-file-in-a-single-sequence-read-like-a-reference-genome/13208)
**Author:** [@Matee\_Ullah](https://help.galaxyproject.org/u/Matee_Ullah)\ **Replies:** 1\ **Last updated:** [August 13, 2024, 5:59pm UTC](https://help.galaxyproject.org/t/how-to-make-fasta-file-in-a-single-sequence-read-like-a-reference-genome/13208 "2024-08-13T17:59:28Z")
Hello I hope all are doing well. I have a query about how to make fasta file into a single read. In the below pic you can see the file is fasta but the sequence read is separated . I want to make them like a reference … --- ## [Troubleshooting: BlobToolKit error after Diamond](https://help.galaxyproject.org/t/troubleshooting-blobtoolkit-error-after-diamond/12967)
**Author:** [@chuan\_zhai](https://help.galaxyproject.org/u/chuan_zhai)\ **Replies:** 3\ **Last updated:** [July 16, 2024, 4:06am UTC](https://help.galaxyproject.org/t/troubleshooting-blobtoolkit-error-after-diamond/12967 "2024-07-16T04:06:27Z")
Hi! I met a problem when following the post-assembly-QC-workflow: Hands-on: ERGA post-assembly QC / ERGA post-assembly QC / Assembly Here is the error message when I runed the BlobToolKit within this workflow: Traceba… --- ## [N50 statistic for rnaviralSPades](https://help.galaxyproject.org/t/n50-statistic-for-rnaviralspades/12907)
**Author:** [@Serkan\_ONDER](https://help.galaxyproject.org/u/Serkan_ONDER)\ **Replies:** 2\ **Last updated:** [July 10, 2024, 12:28pm UTC](https://help.galaxyproject.org/t/n50-statistic-for-rnaviralspades/12907 "2024-07-10T12:28:58Z")
Dear All, do you have any idea about how could I see N50 statistic after denovo assembly via rnaviralSPades in Galaxy Europe?. I have already tried to include log, contigstat and scaffoldstat options as output during the… --- ## [Number of polishing iterations in Flye assembly and Pseudogene count](https://help.galaxyproject.org/t/number-of-polishing-iterations-in-flye-assembly-and-pseudogene-count/12905)
**Author:** [@l.r.l.s.k](https://help.galaxyproject.org/u/l.r.l.s.k)\ **Replies:** 2\ **Last updated:** [July 10, 2024, 7:10am UTC](https://help.galaxyproject.org/t/number-of-polishing-iterations-in-flye-assembly-and-pseudogene-count/12905 "2024-07-10T07:10:16Z")
Hello, I was following the tutorial of Hands-on: Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data) / Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumin… --- ## [Error when parsing assembly graph data in Bandage Image](https://help.galaxyproject.org/t/error-when-parsing-assembly-graph-data-in-bandage-image/12784)
**Author:** [@Manuel1](https://help.galaxyproject.org/u/Manuel1)\ **Replies:** 2\ **Last updated:** [June 26, 2024, 7:46am UTC](https://help.galaxyproject.org/t/error-when-parsing-assembly-graph-data-in-bandage-image/12784 "2024-06-26T07:46:55Z")
Dear Galaxy Users, I am new to genome analyses and was running through some of the tutorials to get familiar with the functionalities and workflows in Galaxy. Whilst running through the De Bruijn Graph Assembly tutorial,… --- ## [complete chromosome sequence](https://help.galaxyproject.org/t/complete-chromosome-sequence/12790)
**Author:** [@S\_K\_A](https://help.galaxyproject.org/u/S_K_A)\ **Replies:** 1\ **Last updated:** [June 25, 2024, 11:27pm UTC](https://help.galaxyproject.org/t/complete-chromosome-sequence/12790 "2024-06-25T23:27:56Z")
Hello, can anyone please suggest the tool to find out if my whole genome sequence has any complete chromosome sequence as this data asked on NCBI Genome submission? --- ## [Getting high number of pseudogenes](https://help.galaxyproject.org/t/getting-high-number-of-pseudogenes/12539)
**Author:** [@l.r.l.s.k](https://help.galaxyproject.org/u/l.r.l.s.k)\ **Replies:** 1\ **Last updated:** [May 20, 2024, 7:24pm UTC](https://help.galaxyproject.org/t/getting-high-number-of-pseudogenes/12539 "2024-05-20T19:24:55Z")
Hi, I have done whole genome assembly of nanopore reads with flye and annotation using Prokka. However i got 30x coverage assembly file, it’s containing more than 2k pseudogenes. Can anyone suggest a tool to remove pseu… --- ## [Assembly of single-end and paired-end sequences](https://help.galaxyproject.org/t/assembly-of-single-end-and-paired-end-sequences/12438)
**Author:** [@Sanji](https://help.galaxyproject.org/u/Sanji)\ **Replies:** 5\ **Last updated:** [May 13, 2024, 3:53pm UTC](https://help.galaxyproject.org/t/assembly-of-single-end-and-paired-end-sequences/12438 "2024-05-13T15:53:14Z")
Can I assemble the paired-end and single-end sequences separately and then use staramr to obtain their ARGs information together? This is because my fastq files contain both paired-end and single-end sequences. --- ## [Flye crashed with out of memory error](https://help.galaxyproject.org/t/flye-crashed-with-out-of-memory-error/12472)
**Author:** [@chrisbioinfo](https://help.galaxyproject.org/u/chrisbioinfo)\ **Replies:** 3\ **Last updated:** [May 13, 2024, 3:49pm UTC](https://help.galaxyproject.org/t/flye-crashed-with-out-of-memory-error/12472 "2024-05-13T15:49:51Z")
Hello, I was trying to assemble some ONT data with flye, and the job crashed with what looks like out of memory errors based on the logs. Can you set memory limits for jobs in Galaxy? Im attaching the history here for … [Next page](https://help.galaxyproject.org/tag/assembly/75.md?match_all_tags=true&page=1&tags%5B%5D=assembly)