M2 Lab2 - areed37/Andrew_Reed_EPP_531 GitHub Wiki

#our group for the hifi was 80x

#fasta output hifi 1700 0.4 hap2
awk '/^S/{print ">"$2;print $3}' Sassafras_V1.0_with_Hi-C_1700_0.4_group.hic.hap2.p_ctg.gfa > Sassafras_V1.0_with_Hi-C_1700_0.4_group.hic.hap2.p_ctg.fasta
#stats hifi 1700
/sphinx_local/software/bbmap/stats.sh -Xmx10g in=Sassafras_V1.0_with_Hi-C_1700_0.4_group.hic.hap2.p_ctg.fasta > Sassafras_V1.0_with_Hi-C_1700_0.4_group.hic.hap2.p_ctg.stats.txt

/sphinx_local/software/hifiasm/hifiasm \
-o Sassafras_V1.0_with_Hi-C \
-t 2 \
-s 0.40 \
--hg-size 1700 \
--h1 salbidum01_1334141_S3HiC_R1.fastq.gz \
--h2 salbidum01_1334141_S3HiC_R2.fastq.gz \
sassafras_samtools_HiFI_reads.fq \
>& hifiasm_output_0.4_.txt