Hi-C~SALSA

SALSA: A tool to scaffold long read assemblies with Hi-C

input_1:paired-end FASTQ(.gz) files

input_1/L2HATA_1.fq.gz

input_1/L2HATA_2.fq.gz

input_2:reference genome file

input_2/hatahifihic.hic.p_ctg.gfa.fa

input_3:bwa index

Command

Hi-C~SALSA -c 16 input_1/ input_2/hatahifihic.hic.p_ctg.gfa.fa

Output

SALSA_HiC/scaffolds_FINAL.fasta

>scaffold_1
GTTGGAAAGTAACAGCCTAAATGACAACATGCTCTCAAAATGCTTCTCTCGGGCCGAAAAGCTCAAAAGTGACATTTTGC
TGTTTTCTGACCAACTACTGATGGGACCTACATGAAACTGCCCTGGTAGTGTAGAATTCATCAAATCACACGTTTCTGGC
TTGAAAACTTGTTTCTGAGTGCTTCTGTTGGAAAAGTAACAGCCCTAAATGACAACATGCTCTCAAAATGCTTCTCTCGG
GCCGAAAAGCTCAAAAGTGACATTTTGCTGTTTTCTGACCAACTACTGATGGCAACTACATGAAACTGCCCTGGTAGTGT
AGAATTCATCAAATCACACGTTTCTGGCTTGAAAACTTGTTTCTGAGTGCTTCTGTTGGAAAGTAACAGCCTAAATGACA
ACATGCTCTCAAAATGCTTCTCTCGGGCCGAAACGCTCAAAAGTGACATTTTGCTGTTTTCTGACCAACTACTGATGGGC
AACTACATGAAACTGCCCTGGTAGTGTAGAATTCATCAAATCACACGTTTCTGGCTTGGAAACTTGTTTCTGAGTGCTTC
TGTTGGAAAGTAAACAGCCTAAATGACAACATGCTCTCAAAATGCTTCTCTCGGGCCGAAAAGCTCAAAAGTGACATTTT
GCTGTTTTCTGACCAACTACTGATGGGACATACATGAAACTGCCCTGGTAGTGTAGAATTCATCAAATCACACGTTTCTG

SALSA_HiC/salsa_scaffolds.hic

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Log