BOL: Results for "bioawk"

Results for "bioawk"

- Neelam Jha@neelam
Converting FASTQ to FASTA
...STDIN. [-o OUTFILE] = FASTA output file. default is STDOUT. Bioawk Another option to convert fastq to fasta format using bioawk bioawk -c fastx '{print ">...
2300 days ago

- Jit@jit.aber
Find a pattern in first 7 characters of reads. bioawk -c fastx 'substr($seq,0,7) == $TAG { print }' reads.fq.gz #Reads #NGS #Extract #Pattern
2496 days ago

- Jit@jit.aber
FASTQ to FASTA
...| awk '{if(NR%4==1) {printf(">%s\n",substr($0,2));} else if(NR%4==2) print;}' > file.fa #seqtk seqtk seq -a input.fastq > output.fasta #Bioawk bioawk -c fastx '{print ">"$name"\n"...
845 days ago

- Aaryan Lokwani@aaryan
Comment on "Most Commonly used Awk by Bioinformatician"
I love awk but recommend you to try bioawk . Bioawk is a modified version of awk which will parse some common sequence formats. https://github.com/lh3/bioawk
3676 days ago
- Jitendra Narayan@admin
Comment on "Most Commonly used Awk by Bioinformatician"
There is BioAwk, specially designed for bioinformatician by ialbert. .... https://github.com/ialbert/bioawk-tools Njoy
3903 days ago