Results for "NGS READGROUPS GATK FastQ"
Bio-Scripts
Rules to run fastp / Snakemake !
rule fastp: input: fwd=INPUT + "/{sample}-read_1.fq",...rev=INPUT + "/{sample}-read_2.fq" output: fwd=RESULTS + "/fastq_trimmed/{sample}.1.trimmed.fastq", rev=RESULTS + "/fa...928 days ago
- #GATK is a toolkit developed by the broad institute focused primaril...e. First let’s download and unzip GATK from github. The creators of GATK recommend running GATK throug...create a virtual environment for GATK by using the yaml file includ...https://github.com/broadinstitute/gatk/...
838 days ago
Bash command to count reads in fastq file !
#ref fastq file #ref1_1.fq) echo $(( $(wc -l818 days ago
Raku script to find SSRs in fastq file !
sub find-ssrs(Str $sequence) { my @ssrs; for...} } return @ssrs; } sub process-fastq-file(Str $filename) { my...} } $fh.close; } # Replace 'your_fastq_file.fastq' with the path to...139 days ago
- seqtk seq -F '#' in.fa > out.fq # "#" is fake score.
75 days ago
Python script to convert fastq to fasta
def fastq_to_fasta(fastq_file, fasta_file): with open(fastq_file, 'r') as fq: with open(fast...# Read four lines from the FASTQ file header...rite(sequence + '\n') # Usage example fastq_to_fasta('input.fastq', 'outp...65 days ago
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