Questions tagged [assembly]
Process of creating the original sequence from the read sequences that it generated during a sequencing experiment. Can refer to genome assembly, in which case the original sequence is a genome, or transcripts assembly, in which case the original sequences are RNA transcripts.
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wtdbg2: practical implications of k-mer fsize and psize choice
I am using wtdbg2 2.3 to assemble a human genome (sequenced on PromethION from a cell line). I filtered out reads with low average quality, and now I am trying to determine the parameters that will ...
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How is consensus alignment for OLC assembly usually implemented?
Background
In C++ I want to implement a simple class that performs overlap layout consensus assembly but I can not figure out the most logical data structure to use for the consensus alignment step.
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Calculating alignment/mapping time
I am trying to assemble a plant genome using AWS resources using velvet. Plant genome is huge (> 10 times human genome) and coverage is around 30 x. We are planning for de novo assembly with Velvet (...
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E.coli Sequencing & Analysis
I have been given the task of assembling a 'new' Ecoli genome and analysing the genes present etc.
The Ecoli is a new strain, and has been taken and run on a Nextseq 500 in high-output mode with ...
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Problem with SPAdes installation - no bin folder
I have been trying to download SPAdes for an important project I wanted to do, however, I have encountered a small problem while doing so. It appears that there is no 'bin' folder in my SPAdes ...
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How many reads do I need for hybrid assembly
I have Illumina and PacBio reads and I would like to use dbg2olc for hybrid assembly.
Part of dbg2olc is SelectLongestReads which select reads that sum to ...
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How to assess the quality of assembled .fasta genome files?
I have assembled 3 .fasta files from contigs infastq format of 3 different Homo sapiens.
I would like to see if the assembled ...
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estimate genome size: kmer-based approach from PacBio reads
Can anyone suggest a software/method for kmer analysis using PacBio reads (RSII)?
Something similar to Jellyfish, that I saw in a nice tutorial - but must be suitable for long, noisy reads. ...
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What is the current state-of-the-art in assembling hybrid transcriptomes?
We are considering attempting de novo assembly of a species transcriptomes (i.e. without a reference genome) using the combined NGS outputs of Iso-seq and Illumina.
One example I saw (Li et al 2017),...
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Merge / Reconciliate several de novo transcriptome assemblies with different kmers
I am building a De Novo transcriptome reference assembly for an eukaryotic organism for which I have a genome.
I've created several assemblies with rnaSpades using different kmer sizes (19 to 69 with ...
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Find paralogs in a draft genome
We generated a (diploid, chordata, highly heterozgous) genome using PacBio and we wanted to see whether it contains lineage-specific duplications (paralogs, basically). The genome is not in Ensembl ...
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Reduce number of transcripts in a highly variable de novo transcriptome assembly
I have a de novo assembly using both multiple SRA and locally sequenced transcriptomes. I started with 270M PE reads from 9 tissues. Here are the assembly stats generated with ...
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Correct way to assemble reference transcriptome - what's --samples_file option in Trinity?
I have 101 samples from 9 tissues of a nonmodel species, coming either from SRA or sequenced by my lab. I want to generate a reference transcriptome with Trinity for further analysis. In order to do ...
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Viral Metagenomics
I am analyzing viral metagenomics data (Illumina Miseq) for the first time. I have used Ray (reference below) for de novo viral genome assembly before but I haven't done metagenomics analysis before.
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Why isn't there a standard method to convert GFA to JSON?
I'm confused why the GFA format doesn't have a standard JSON parser. It appears to be related to a decision made several years ago, here.
The objection appears to be "JSON isn't necessary, as it's ...
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Is there a standard definition for "assembly polishing"?
Is there a standard definition for "assembly polishing" in the field?
Is there a standard definition for what polishing algorithms do?
My understanding of "polishing" is strongly influenced by ...
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Does the galGal5 chicken assembly have a chromosome 29?
The chromosome sizes at UCSC don't seem to contain chr29:
ftp://hgdownload.soe.ucsc.edu/goldenPath/galGal5/bigZips/galGal5.chrom.sizes
It has a chr28 and a chr30. Am I missing something or is there ...
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Cufflinks Error: sort order of reads in BAMs must be the same
I am running Cufflinks for transcriptome assembly using the .bam file generated by Hisat2. I tried both bam and sorted bam files
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Why can using more reads lead to a lower quality assembly?
I am experimenting with adding additional reads to the input files I'm giving SOAPdenovo2, and there comes a point where a good contig I've been watching actually stops showing up. Does anyone have a ...
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Make ipyrad use cuda-enabled NVidia card on Ubuntu
I want to use ipyrad on a new Ubuntu machine that has an NVidia Quadro K2000 card with 384 cores. One can configure ipyrad to run on a linux cluster. Do I have any options to get ipyrad to access ...
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Difference between de novo transcriptome assembly methods
I have been looking around (including read the original papers) to understand what is essentially the difference between StringTie in non-reference based mode (de novo) and Trinity de novo assembly. I ...
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Can the canu assembler output a fastq file of the final assembly just like HGAP4?
I have assembled some genome from Sequel PacBio data both with HGAP4 on the SMRT Link interface and using canu on the command line. The HGAP4 assembler outputs a fastq file of the final assembly such ...
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SPAdes error during assembly
I try to perform a hybrid assembly using Unicycler. Unicycler use SPAdes to assembly the illumina sequences, and the program crashes while in SPAdes. The spades.log file says something about an ...
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Scaffolding a genome with hybrid data
I am assembling a ~500MB genome, and have ~150x long reads and ~200x 150bp PE short reads, with a ~400bp insert size.
I've done a lot of work with minimap+miniasm, and have what I think is a good set ...
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How to submit a canu job on LSF high-performance computing cluster farm?
I am currently running canu on an LSF Linux server using the following script called assemble.sh:
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Java error when launching Pilon
I am trying to use Pilon to improve a reference based on some Illumina data I have got. So, I aligned the Illumina reads to the reference using bwa. Then, I want to use Pilon to improve the reference ...
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Verify a predicted protein in one genome in a different genome of the same species
I have two genome assemblies of the same non-model species, call them Assembly 1 (generated from Illumina data) and Assembly 2 (generated from PacBio data).
For Assembly 1, I also have predicted ...
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Genome assembly from error-prone reads
I understand how to assemble genome from error-free reads. I implemented like this:
Construct directed overlap graph with reads as vertices and edges as
maximum overlap between two vertices. ...
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How to calculate overall reference coverage with MUMmer?
Is the MUMmer suite capable of calculating reference sequence coverage statistics for all query sequences collectively? It would be possible to achieve by parsing the output of ...
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Reordering scaffolds according to a reference without a genetic map
I am trying to reorder scaffolds of a rice species, but no genetic map is available right now. Oryza sativa Japonica is a close relative of this rice species. Mummer was used to do a whole genome ...
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PASA pipeline: compare experimental transcripts to the reference annotation
I would like to ask if anyone has experience in running a subset of the PASA pipeline, in particular for the reconciliation of some experimental 'transcripts' with the reference annotation.
In more ...
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Pooling data in metagenome assembly
I have 12 human gut microbiome WGS Nextseq reads (151 bp paired end). What will be an effective strategy to assemble a metagenome?
Let us say I have already filtered the fastq for quality, adapter ...
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Assembling sequence data generated by RADseq [closed]
I'm working on a project where I have to assemble sequences generated by RADseq. At the end I hope to compare two species of woodpeckers in Sri Lanka by using SNPs.
I tried to assemble it using ...
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What causes the difference in total length of assembled contigs and scaffolds in SOAPdenovo2?
I use SOAPdenovo2 to assemble a large genome (4.8G) using ~20X paired-end reads. The total length of contig sizes is 6.3G while total length of scaffolds is 2.7G. Note that this is a haploid genome, ...
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How can I improve a long-read assembly with a repetitive genome?
I'm currently trying to assembly a genome from a rodent parasite, Nippostrongylus brasiliensis. This genome does have an existing reference genome, but it is highly fragmented. Here are some ...
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How to deal with heterozygosity during polishing of genome assembly based on long reads?
All the long-read sequencing platforms are based on single-molecule sequencing which causes higher per-base error rates. For this reason a polishing step was added to genome assembly pipelines - ...
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Why do some assemblers require an odd-length kmer for the construction of de Bruijn graphs?
Why do some assemblers like SOAPdenovo2 or Velvet require an odd-length k-mer size for the construction of de Bruijn graph, while some other assemblers like ABySS are fine with even-length k-mers?
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How to make a distinction between the "classical" de Bruijn graph and the one described in NGS papers?
In Computer Science a De Bruijn graph has (1) m^n vertices representing all possible sequences of length n over ...
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Improve a reference genome with sequencing data
I have a DNA sample which I know doesn't quite match my reference genome - my culture comes from a subpopulation which has undergone significant mutation since the reference was created.
The example I ...
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