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HiC scaffold
A snakemake workflow that scaffold assembly using Hi-C data
To run
snakemake --cores [cpu] --use-conda
Code Snippets
6 7 8 9 | shell: """ cp {input} {output} """ |
19 20 21 22 23 | shell: """ bwa index {input} samtools faidx {input} """ |
38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 | shell: """ bwa mem \ -t {threads}\ {input.assembly} \ {input.R1}| \ samtools view -@ {threads} -Sb - \ > {output.R1_mapped} bwa mem \ -t {threads}\ {input.assembly} \ {input.R2}| \ samtools view -@ {threads} -Sb - \ > {output.R2_mapped} """ |
65 66 67 68 69 70 71 72 73 74 75 | shell: """ samtools view -h -@ {threads} {input.R1_mapped} | \ filter_five_end.pl | \ samtools view -Sb -@ {threads} - \ > {output.R1_5endFiltered} samtools view -h -@ {threads} {input.R2_mapped} | \ filter_five_end.pl | \ samtools view -Sb -@ {threads} - \ > {output.R2_5endFiltered} """ |
90 91 92 93 94 95 | shell: """ two_read_bam_combiner.pl {input.R1_5endFiltered} {input.R2_5endFiltered} samtools {params.mapq_filter} | \ samtools view -bS -@ {threads} -t {input.fai} - | \ samtools sort -@ {threads} -o {output} """ |
107 108 109 110 111 112 113 114 115 116 117 | shell: """ picard MarkDuplicates \ -Xmx{params.mem} -XX:-UseGCOverheadLimit \ INPUT={input} \ OUTPUT={output.bam} \ METRICS_FILE={output.metric} \ ASSUME_SORTED=TRUE \ VALIDATION_STRINGENCY=LENIENT\ REMOVE_DUPLICATES=TRUE """ |
128 129 130 131 | shell: """ samtools sort -@ {threads} -o {output} -n {input} """ |
15 16 17 18 19 20 21 22 | shell: """ yahs \ --no-contig-ec \ --no-mem-check \ -o {params.prefix} \ {input.assembly} {input.bam} """ |
34 35 36 37 38 39 40 41 | shell: """ (juicer pre {input.bin} {input.agp} {input.fai} | \ sort -k2,2d -k6,6d -T ./ --parallel={threads} -S24G | \ awk 'NF' \ > alignments_sorted.txt.part) \ && (mv alignments_sorted.txt.part {output}) """ |
50 51 52 53 54 | shell: """ samtools faidx {input} cut -f 1,2 {input}.fai > {output} """ |
66 67 68 69 70 | shell: """ (java -jar -Xmx24G {params.juicer_tools_jar} pre {input.aln} out.hic.part {input.chrom_size}) \ && (mv out.hic.part {output}) """ |
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Created: 1yr ago
Updated: 1yr ago
Maitainers:
public
URL:
https://github.com/ZexuanZhao/Hi-C-scaffolding
Name:
hi-c-scaffolding
Version:
1
Downloaded:
0
Copyright:
Public Domain
License:
None
- Future updates
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