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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Why is RNASpades giving three FASTA output files instead of only one?
I'm running RNASpades for de-novo transcriptome assembly in the Galaxy workflow manager
. Instead of giving only one output of ...
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Assessing the quality of an assembly
I am trying to run a script that assess the quality of a transcriptomic assembly, a de novo assembly using a tool called Transrate. To install the tool I followed the prompts in https://bioconda....
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Sanger sequencing annotation error
I am a student in a Cancer lab. Working with sanger is new to me. While analyzing a report we found an insertion that has not been reported in any databases so far, we were working on checking if the ...
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Will using smaller kmers help get larger contigs? If not, then what?
I've been using MEGAHIT to assemble metagenomes, with particular focus on specific genomic areas.
Sometimes all I get is gene fragments or pathway fragments (eg. if I know that genes A, B, C, D and E ...
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Where to find the homopolymer regions bed file for Hg002 genome?
This question was also asked on Biostars
I am doing an experiment where I am trying to analyze the errors in the homopolymer regions between the polished reference hg002 genome and hifiasm assembly ...
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Multiple genome assemblies of the same bacterial species
I have some RNA-seq data where there are reads from the "host" as well as from several bacteria species. In this experimental context, I am interested in the host associated reads and the ...
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Hybrid assembly versus polishing for hifi and illumina reads
I will have to carry out a project of assembly using hifi reads for which I have already illumina reads and I am wondering which of the hybrid assembly or polishing would be the best option for this ...
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How to promote assemblies into genomes in NCBI?
Note: I've never submitted an assembly/genome to NCBI, so excuse if my perspective is flawed.
I'm working with Drosophila subobscura. (spring fruit fly)
I see here https://www.ncbi.nlm.nih.gov/data-...
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Longstitch error make: command: Command not found *** No rule to make target
I installed Longstitch and ran the test script with no issues. The output files matched the expected output files. But when I am now trying to run Longstitch on my own data I am getting this error.
<...
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bwa mem hangs after a few thousand reads
I am trying to align a bunch of paired sample fastq files using bwa mem.
My original command was:
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MMSeqs taxonomy running for over a day
I've been trying to run mmseqs2 on a few metagenomic assemblies and despite my best efforts in reading the wiki and playing with parameters, the process is taking over a day.
In their paper they claim ...
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Why do we delete scaffolds shorter than 500 - 1000 bp from the assembled genome?
After assembly of genome, some protocols sometimes call for removal of scaffolds shorter than 500 or 1000 (some papers have one number while the other has the other.) Is this simply to remove the ...
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Determining fragment mean and fragment stdev for MaSuRCA config file
Similar to this unanswered question on Biostars, I am using MaSuRCA for the first time and want to know how other MaSuRCA users are determining fragment mean and fragment stdev. My understanding is ...
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Interpreting GFA graph visualized in Bandage
I assembled Nanopore sequenced reads with Flye and visualized the GFA graph in Bandage but I don't really know how to interpret the result. For context, this is a yeast (DNA) genome. My goal is to ...
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