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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34
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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?
8
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2answers
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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. ...
2
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2answers
371 views

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 ...
0
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1answer
38 views

Optimum parameters for genome assembly via canu

I have been trying to assemble my genome via canu. Canu gave me about 200 contigs using default parameters. My genomesize is ~9Mbp. Can you recommend some parameters I can tweak to decrease the ...
0
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1answer
72 views

Can I get longer contigs by changing MEGAHIT settings?

My current settings are megahit -r input.fq --num-cpu-threads 32 --min-contig-len 300 --presets meta-large -o output. I picked the 'presets meta-large' because I am ...
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2answers
153 views

What assembler is appropriate for High-Fidelity PacBio reads

What assembler is appropriate for High-Fidelity PacBio reads? For example, canu is good for high-error PacBio reads. But what algorithm to use for HiFi reads? Would it be OK to use canu without the ...
0
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1answer
39 views

mapping and de novo assembly of plant without reference genome

I'm studying on a plant that has no reference genome and only has one scaffold assembly and one gff3 annotation file. Can I create an index with the same assembly and gff3 in STAR and do the mapping? ...
0
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1answer
180 views

nanopore - where to retrieve information from the basecaller used

Where can I find information about the basecaller used in a specific nanopore run (we have a Gridion machine)? I know already that we have Guppy v. 3.0.3, which I ...
2
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2answers
33 views

fixing chromosome with new contig

I want to fix a chromosome of around 50-100Mb (chr.fasta) for a region that is missing a few kilobases of data. I have the missing sequence with a window upstream ...
5
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3answers
2k views

How to get fasta alignment file from SAM/BAM file?

I am not talking about consensus sequence, I know how to get consensus sequence using mpileup in samtools/bcftools. As I understand , SAM/BAM files are basically sequence alignment format so it's ...
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45 views

How to obtain the extended unaligned bases of the read in reference based genome assembly?

I did illumina read mapping based on a particular gene sequence (reference sequence) using the following command, ...
0
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2answers
378 views

Determining the quality of a publicly available genome assembly

I am looking for homologous genes in various protozoan species using BLAST. The genome sequences of these species are deposited in NCBI's WGS database. NCBI’s webpage includes the global statistics ...
3
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1answer
146 views

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 ...
4
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1answer
65 views

Authoritative source on human cytogenetic regions?

I am looking for a database that would keep track of human cytogenetic regions and genomic coordinates per genome assembly. I had expected the Genome Reference Consortium to have it, or Ensembl, or ...
2
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1answer
336 views

Consensus sequence from SAM or BAM file?

I am trying to perform reference-based assembly. Most of the tutorials teach how to create a bam file and view alignemnts in IGV or Tablet. But, I want a assembled genome sequence in fasta format. How ...
1
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1answer
58 views

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 ...
5
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1answer
86 views

Is there a way to assemble contigs starting from a specific sequence?

My work involves searching for marker genes/fragments in metagenomic databases (like the Sequence Read Archive). Once I find these sequences, I would like to know more about the neighboring genomic ...
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1answer
31 views

Is there a resource where I can donwload E. coli assemblies grouped by their pathotypes?

I will preface this by saying I'm not a microbiologist, so I apologise for any haziness and I'll be happy to expand. I would like to download the assemblies of different E. coli genomes and group ...
0
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1answer
402 views

Assembly by stringtie

I run this cmd ./stringtie G1_sorted.bam -B -o G1.gtf -G Triticum_aestivum.IWGSC.42.gtf -p 4 -C G1.refs.gtf -A G1.abund.tab Error is: ...
2
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1answer
366 views

Is nanopolish worth it since faster polishing software is available?

For Oxford Nanopore contigs produced by any long-read assembler has anyone performed any benchmarks to compare the polishing tools racon, ...
3
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2answers
153 views

Separation of mixed plasmid DNA sequences post whole-plasmid sequencing

Imagine a DNA sample containing a mixture of different intact plasmids. These samples are sequenced using either MiSeq or HiSeq sequencing. Would it possible to assemble these plasmids post-sequencing ...
2
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1answer
125 views

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. ...
14
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3answers
399 views

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 ...
17
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1answer
529 views

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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0answers
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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 (...
2
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1answer
156 views

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 ...
0
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1answer
62 views

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 ...
5
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1answer
120 views

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 ...
5
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2answers
265 views

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 ...
2
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1answer
94 views

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 ...
4
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1answer
83 views

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 ...
8
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2answers
962 views

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 ...
0
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1answer
136 views

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 ...
6
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1answer
305 views

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 ...
3
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1answer
385 views

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 ...
4
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1answer
68 views

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 ...
9
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3answers
454 views

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 ...
5
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3answers
68 views

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 ...
5
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2answers
776 views

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 ...
3
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1answer
121 views

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 ...
3
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0answers
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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 ...
3
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1answer
120 views

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 ...
3
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0answers
184 views

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: ...
2
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0answers
66 views

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 ...
6
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1answer
149 views

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 ...
11
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5answers
302 views

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. From visual ...
6
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2answers
171 views

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. ...
7
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1answer
200 views

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 ...
4
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2answers
321 views

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 ...
5
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1answer
245 views

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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