New Module: Asset

[mahesh-panchal]

Which tool should be included? https://github.com/dfguan/asset

How is it used?

# Find Gaps
bin/detgaps $asm > $output_dir/gaps.bed

# Process Pacbio data
for fl in $pblist
do
    minimap2 -xmap-hifi -t 12 $asm $fl > $fl.paf
done

bin/ast_pb $fl1.paf $fl2.paf $fl3.paf ... >$output_dir/pb.bed 2>ast_pb.log

# Process Hi-C data 
bin/split_fa $asm > split.fa
samtools faidx split.fa 
bwa index split.fa
while read -r r1 r2
do
    prefix=`basename $r1 .fq.gz`
    dirn=`dirname $r1`
    bwa mem -SP -B10 -t12 split.fa $r1 $r2 | samtools view -b - > $dirn/$prefix.bam
done < $hiclist
bin/col_conts *.bam > $output_dir/links.mat
bin/ast_hic2 split.fa.fai $output_dir/links.mat >$output_dir/hic2.bed 2>ast_hic.log

# Accumulate evidence
bin/acc $output_dir/gaps.bed $output_dir/{pb,bn}.bed $output_dir/bn.bed > $output_dir/pb_bn.bed 
bin/acc $output_dir/gaps.bed $output_dir/{10x,hic2,bn}.bed > $output_dir/10x_hic2_bn.bed  

# Detect misassemblies
bin/pchlst -c $output_dir/gaps.bed $output_dir/pb_bn.bed > $output_dir/pchlst_ctg.bed
bin/pchlst $output_dir/gaps.bed $output_dir/10x_hic2_bn.bed > $output_dir/pchlst_scaf.bed 
bin/union_brks $output_dir/gaps.bed $output_dir/pchlst_{ctg,scaf}.bed > $output_dir/pchlst_final.bed

Which workflow should it be included in?

Curation