Looks like ABYSS expects a fastq formatted file, while your file is fasta formatted:
http://en.wikipedia.org/wiki/FASTQ_format
http://en.wikipedia.org/wiki/FASTA_format
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Also, you should write an email to the ABySS-users list. The authors of ABySS read the list and are very helpful.Leave a comment:
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Interestingly, I am having the same issue. As a sanity check I'm attempting to reassemble some contigs produced by ABySS. I'm not sure what the parser expects to read and the error message doesn't print the location of the error in the file.Leave a comment:
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Abyss @ 454
Hi there,
Is ABYSS designed for assembly of 454 reads?
# ./ABYSS -k25 -o /data/454/data/_Test_assembly /data/454/data/2.TCA.454Reads.fna
gives me the following
2.TCA.454Reads.fa' is an unknown format
Expected either `>' or `@' or 11 fields
and saw `C' and 1 fields
?
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Amplicon sequencing is a targeted approach that allows researchers to investigate specific regions of the genome. This technique is routinely used in applications such as variant identification, clinical research, and infectious disease surveillance. The amplicon sequencing process begins by designing primers that flank the regions of interest. The DNA sequences are then amplified through PCR (typically multiplex PCR) to produce amplicons complementary to the targets. RNA targets...03-21-2023, 01:49 PM -
Targeted sequencing is an effective way to sequence and analyze specific genomic regions of interest. This method enables researchers to focus their efforts on their desired targets, as opposed to other methods like whole genome sequencing that involve the sequencing of total DNA. Utilizing targeted sequencing is an attractive option for many researchers because it is often faster, more cost-effective, and only generates applicable data. While there are many approaches...03-10-2023, 05:31 AM
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