abyss assembler

Question

[erikatatianacs]

Hello, I had been trying to asseble de novo a human genome from WGS. The problem that I had is that when I check the results: test-contigs.fa I just found I few lines. I dont get any error, I dont really know what is the problem. I check the samples and they look ok.

cat SRR6345720_1_paired.fastq.gz | head -n 10

@SRR6345720.1 1 length=128
TGCACACCGATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAACCGGAAGCGCACACTAC
+SRR6345720.1 1 length=128
JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJFJFJ-A-F7-A77-7-7A<J--7
@SRR6345720.2 2 length=128
CTAACTTTCCACATCGATAACCCTAACCCTAACCCTAACCCTAACCCTAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAA
+SRR6345720.2 2 length=128
AJFF7JJJA-FJJFAJFJJJJFJFJJFJFFJFJ<A7FJJAJFFJJJAJJJFJFJ7--7F-<A-7-AJAF-AA<JFFAJ7AJFFAF7<
@SRR6345720.3 3 length=128
ATCGACTGACGCTCTTCCGATCTCTACGTCAGTCGATAACCCTAACCCTAACCCTAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGTCATCATCTCGTATGCCGTCTTCTGCTTGAAAAA

cat SRR6345720_2_paired.fastq.gz | head -n 10

@SRR6345720.1 1 length=151
AGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTATCGGTGTGCACGAAGAGTTCGTGCACACCGATTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAA
+SRR6345720.1 1 length=151
AAFFFJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJFAJ<FAJJFJFJ<7AJJJJ<AAFJJFF7JJJFJAFFFJJJFJ<7A-FFAJJJF<AFJJ<FFAJAAFFFFJJJF)-A<FJ-A-<AF7F<AAFF
@SRR6345720.2 2 length=151
GTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTATCGATGTGGAAAGTTAGATCGCCGATCGATGTGGAAAGTTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAA
+SRR6345720.2 2 length=151
AAAFFFJJJFJJJFAJJJJJJJJJFJJJFJJFJJJJJ-FFFJF-FJFFFJFJJJJJFJAJJJAAJJJJJFJFJJJAJJFJFJFJFJJJ<7AFFAFFJJ-7FFJJFFJJFFA<A<AFFAFA7<7FAFF7<AAFA<-F7
@SRR6345720.3 3 length=151
TAGGGTTAGGGTTAGGGTTATCGACTGACGTAGAGATCGGAAGAGCGTCAGTCGATAACAACATTATCGACTGACGTAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAA

These are the parameters

abyss-pe k=50 name=test B=80G \
    in='SRR6345720_1_paired.fastq.gz SRR6345720_2_paired.fastq.gz

Answer 1

[colindaven]

This is a different type of library, it is not a standard paired end Illumina human genome which would work "well " with Abyss.

This is a 10X genomics linked read library. https://www.10xgenomics.com/products/linked-reads

Unfortunately this product has been discontinued. It is probably best to look for other data to test-assemble. Most human genome data are not broadly available, but check genome in a bottle GIAB for open example datasets.

See here https://www.ncbi.nlm.nih.gov/sra/?term=SRR6345720