Results for "Paired end sequencing"
Bio-Scripts
Tadpole is 250x faster than SPADes assembler !
lege@jit-Lenovo-ideapad-320-15ISK:~/Downloads/MyTools/Vir$ tadpole...ounts to assemble contigs, extend sequences, or error-correct re...tadpole.sh in= out= mode=extend Correction: tadpole.sh in= ou...extendleft=100 (el) Extend to the left by at most this m...990 days ago
- blastpgp arguments: -d Database [String] default = nr -...default = 40 -f Threshold for extending hits [Integer] defaul...uery-anchored no identities and blunt ends, 6 = flat query-anchored, n...] default = 11 -E Cost to extend a gap...
964 days ago
Inreractive SCP / File transfer !
#!/bin/bash #next line prints hearer of script echo "Interactive Script to Copy File (files) / Directory using...ation path on destination server scp -r "$filename" "$desthost":"$destpath" #end of if...964 days ago
- # make reference for randomreads.sh # randomreads.sh part of BBTo...=0.13 pbmax=0.17 \ reads=100 paired=f \ gaussianlength=t \ minl...s=t addslash=t \ coverage=30 paired=t maxinsert=550 mininsert=450...# interleave the paired-end reads # reformat.sh part of...
942 days ago
Onliner to convert multi line fasta to single line fasta !
#Oneliner to convert awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);} END {printf("\n");}' < file.fa > fileres.fa #Then delete the first empty line tail -n +2 fileres.fa > fileout.fa942 days ago
Bash script to simulate a genome !
# Reference https://github.com/chhylp123/hifiasm/issues/33 # Use Drosop...=t pbmin=0.13 pbmax=0.17 \ reads=100 paired=f \ gaussianlength=t \ minl...minanames=t addslash=t \ coverage=30 paired=t maxinsert=550 mininsert=...2>&1 # interleave the paired-end reads...931 days ago
- Built-In Variables In Awk Awk’s built-in variables include the field variables—$1, $2, $3, and so on ($0 is t...is a newline character. print automatically outputs the contents of ORS at the end of wha...
908 days ago
Install Varscan on Ubuntu / Linux !
#Varscan is a java program designed to call variants in sequencing data. It was developed at the Genome Institute at Washington University and is hosted on github. To use Varscan we simply need to d...837 days ago
- #!/bin/bash #Counting k-mers for different k echo "k,unique,distinct,total" for k in {1..15}; do kat hist -o phiX_$k.hist -m $k phiX.fasta >/dev/null 2>&1 egrep -v '^#' phiX_$k.hist|awk '{if ($1==1) u=$2; d+=$2; t+=$2*$1;}\ END{print "'$k',"u","d","t}' done
808 days ago
Bash script to convert multiline fasta to single line fasta !
#file.fa is multiline fasta awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);} END {printf("\n");}' < file.fa780 days ago
