Results for "seqtk"

Bio-Scripts

  • Install seqtk using conda !

    vik@vik-Lenovo-ideapad-320-15ISK:~/Downloads/setu/setu$ conda install -c bioconda/label/cf201901 seqtk Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.

    1016 days ago

  • Palindrome Simulation commands !

    .../Tools/art_bin_MountRainier/art_illumina -ss MSv3 -sam -i allPalindromeSimulated.fa -p -l 250 -f 100 -m 300 -s 10 -o paired_dat 3321 ~/Tools/seqtk/seqtk mergepe paired_dat1.fq paired...

    1697 days ago

  • FASTQ to FASTA

    ...-s "/t" "/n" > OUTFILE.fasta #awk cat infile.fq | 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.f...

    812 days ago

  • Running Trinity on RNA-seq !

    ...input files. (both directions in parallel)CMD: seqtk-trinity seq -A /media/urbe/My...ACXX.IND11_noribo_clean.fastq >> left.fa CMD: seqtk-trinity seq -A /media/urbe/My...dir/insilico_read_normalization/left.norm.fq | seqtk-trinity seq -A - >> left.fa...

    2089 days ago

  • Convert FASTQ to FASTQ

    # Convert FASTQ to FASTA seqtk seq -a IN.fastq > OUT.fasta # Convert FASTQ to FASTA and set bases of quality lower than 20 to N seqtk seq -aQ64 -q20 -n N IN.fastq > OUT.fasta # Download Seqtk https://github.com/lh3/seqtk

    1687 days ago

  • Extract the sequence by IDs !

    ...ed directly to FASTA or a FASTQ file, compressed or uncompressed files. Seqtk is a fast and lightweight too...ct sequences with names in file name.list, one sequence name per line: seqtk subseq input.fasta name.list...

    1364 days ago

  • get GC across the entire CDS !

    #look at GC across the entire CDS. gffread -x - -g | \ seqtk comp - | \ awk -v OFS="\t" '{ print $1, "0", $2, ($4 + $5) / $2 }'

    1355 days ago

  • Install seqtk using conda !

    (JitMetaENV) ➜ META_PE conda install -c bioconda seqtk Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.

    1177 days ago

  • Installing Covid19 Environment !

    ...######################################################################################################################################### | 100% seqtk-1.3 | 38 KB |...

    885 days ago

  • Bash script to simulate a genome !

    ...conda activate bcftools1.10.2 # Use Seqtk to convert soft-masked bases...compress with bgzip # https://github.com/lh3/seqtk /genetics/elbers/bin/seqtk/s...upper.diploid.fasta.gz|\ /genetics/elbers/bin/seqtk/seqtk seq -L0|paste - - |grep...

    880 days ago