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Quality assessment of the assemblies¶

Quast assessment for DSM158¶

In [ ]:
quast.py -o ./\
-r ../../GCF_003324715.1_ASM332471v1_genomic.fna \
-g ../../GCF_003324715.1_ASM332471v1_genomic.gff \
-t 20\
--k-mer-stats\
--circos \
--pe1 ../../Autocycler_assembly/reads_qc/illumina_1.fastq.gz \
--pe2 ../../Autocycler_assembly/reads_qc/illumina_2.fastq.gz \
--nanopore ../../Autocycler_assembly/ont_6k.fastq \
../../DSM158_NCBI/DSM158.fasta

Quast assessment for SubH2¶

In [ ]:
quast.py -o ./ \
-r ../../GCF_003324715.1_ASM332471v1_genomic.fna \
-g ../../GCF_003324715.1_ASM332471v1_genomic.gff \
-t 20 \
--k-mer-stats \
--circos \
--single ../../Csph_ShortRead_Seq/SRR5769006.fastq \
--nanopore ../../Csph_LongRead_Seq/SRR10675046.fastq \
../../Trycycler_Assembly/annot_results/trycycler_medaka_polypolish.fasta

Merqury assessment for DSM158¶

In [ ]:
meryl k=21 count illumina_1.fastq.gz output reads_1.meryl
meryl k=21 count illumina_2.fastq.gz output reads_2.meryl
meryl union-sum reads_1.meryl reads_2.meryl output reads.meryl
merqury.sh reads.meryl/ ../../../Autocycler_assembly/final/Cereibacter_sphaeroides_reoriented.fasta DSM158

Merqury assessment for SubH2¶

In [ ]:
meryl k=21 count ../../../Csph_ShortRead_Seq/SRR5769006.fastq  output reads.meryl
merqury.sh reads.meryl/ ../../../Trycycler_Assembly/annot_results/trycycler_medaka_polypolish.fasta Subh2