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.fa963 days ago
Installing Covid19 Environment !
...################################# | 100% font-ttf-ubuntu-0.83 | 1.9 MB | ###...################################# | 100% font-ttf-source-code | 684 KB | ###...################################# | 100% font-ttf-inconsolata | 94 KB | ###...958 days ago
Extract fasta sequences with ids in another file !
#Ids are in test.txt - one ids per line #sequences are in test.fa grep -w -A 2 -f test.txt test.fa --no-group-separator # seqtk seqtk subseq test.fa test.txt #faSomeRecods faSomeRecords in.fa listFile out.fa # seqkit seqkit grep -n -f list.txt sequences.fas > newfile2.fas924 days ago
885 days ago
Installing SEVA environment in Conda !
...######################################################################################################################################## | 100% r-utf8-1.2.1 | 162 KB |...873 days ago
Install Install Gffcompare on Ubuntu / Linux
#Gffcompare is a program that is used to perform operations on general feature format (GFF) and general transfer format (GTF) files. It has a binary distribution compatible with the...858 days ago
Bash script to split multifasta file !
...awk 'BEGIN {n=0;} /^>/ {if(n%500==0){file=sprintf("chunk%d.fa",n);} print >> fi...ksize/10)+1 } /^>/ {if(n%chunksize==0){file=sprintf("chunk%d.fa",n);} print >> fi...hich has the following simple command: gt splitfasta -numfiles 10 multi.fasta858 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.fa801 days ago
Script to rapid genome clustering based on pairwise ANI
...package to perform all-vs-all blastn of sequences: blastn -query -db -outfmt '6 std qlen slen' -max_targ...ll speed up the search at the cost of sensitivity: blastn -query -db -outfmt '6 std qlen slen' -max_targ...670 days ago
627 days ago