SV detection

Purpose

Procedures for read alignment, assembly and SV detection.

Reads alignment

minimap2

## HiFi
minimap2 -a -H -k 19 -O 5,56 -E 4,1 -A 2 -B 5 -z 400,50 -r 2000 -g 5000 -Y --MD 

## ONT
minimap2 -a -z 600,200 -x map-ont -Y --MD 

ngmlr

## HiFi
ngmlr -x pacbio

## ONT
ngmlr -x ont

winnowmap

## HiFi
winnowmap -W ./repetitive_k15.txt -ax map-pb -Y --MD

## ONT
winnowmap -W ./repetitive_k15.txt -ax map-ont -Y --MD

lra

## HiFi
zcat $fastq | lra align -CCS $ref /dev/stdin -t $thread -p s --printMD -SkipH 

## ONT
zcat $fastq | lra align -ONT $ref /dev/stdin -t $thread -p s --printMD -SkipH

Genome assembly

flye

## HiFi
flye --pacbio-hifi

## ONT
flye --nano-raw

shasta

./shasta-Linux-0.8.0 --config Nanopore-Oct2021

hifiasm

hifiasm -o output.tag -l1 input.fqs input.fqs_untag

Assembly alignment

minimap2

The alignment parameters are used in PAV.

minimap2 -x asm20 -m 10000 -z 10000,50 -r 50000 --end-bonus=100 --secondary=no -O 5,56 -E 4,1 -B 5 -a --eqx -Y

LRA

lra global -CONTIG $ref
lra align $ref $hap1 -CONTIG -p s -t $thread > ./hap1.sam
lra align $ref $hap2 -CONTIG -p s -t $thread > ./hap2.sam

SV detection

For all read-based callers, the minimum number of support read is set to 1, 2, 5 and 5 for 5X, 10X, 20X and 35X coverage data, respectively

pbsv

Minimum number of support read is set with parameters -A and -O.

pbsv discover
pbsv call -m 50 -A 5 -O 5 -S 0

SVIM

Minimum number of support read is set with bcftools command bcftools view -i "SUPPORT >= X".

svim alignment --cluster_max_distance 1.4 --min_sv_size 50 

## Minimum number of support read 2 for 10X and 20X coverage data
bcftools view -i "SUPPORT >= 5" variants.vcf > HG002.svim.s5.vcf

cuteSV

Minimum number of support read is set with parameter -s.

## HiFi
cuteSV --min_size 50 -t 6 --max_cluster_bias_INS 1000 --diff_ratio_merging_INS 0.9 --max_cluster_bias_DEL 1000 --diff_ratio_merging_DEL 0.5 -s 5

## ONT
cuteSV --min_size 50 -t 6 --max_cluster_bias_INS 100 --diff_ratio_merging_INS 0.3 --max_cluster_bias_DEL 100 --diff_ratio_merging_DEL 0.3  -s 5 

SVision

Minimum number of support read is set with parameter -s.

SVision -n HG002 -s 5

Sniffles

Minimum number of support read is set with parameter --minsupport.

sniffles --minsvlen 50 --minsupport 5

PAV

snakemake -s Snakefile  -j 28  -k --ri >sublog 2>&1 &

SVIM-asm

svim-asm diploid --tandem_duplications_as_insertions --interspersed_duplications_as_insertions