Workflow Steps and Code Snippets
176 tagged steps and code snippets that match keyword seqtk
Snakemake-based workflow for the assembly of chloroplast genomes
82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 | shell: """ if [ -s {input.genome} ] then mkdir -p {params.dir} for contig in `grep '^>' {input.genome} | sed -e 's/>//g'` do echo $contig > {params.dir}/tmp seqtk subseq {input.genome} {params.dir}/tmp > {params.dir}/$contig.fasta nucmer --maxmatch {input.index} {params.dir}/$contig.fasta -p {params.dir}/out show-coords -THrd {params.dir}/out.delta > {params.dir}/out.coords start=`sort -k6,6hr {params.dir}/out.coords | head -n 1| cut -f3` echo ">$contig" >> {output} echo "$start XXX" if [ $start == 1 ] then grep -v '^>' {params.dir}/$contig.fasta | tr -d '\n' >> {output} echo "" >> {output} elif [ ! -z $start ] then grep -v '^>' {params.dir}/$contig.fasta | tr -d '\n' > {params.dir}/temp.fasta cut -c ${{start}}- {params.dir}/temp.fasta > {params.dir}/start.fasta cut -c -$[start-1] {params.dir}/temp.fasta > {params.dir}/end.fasta cat {params.dir}/start.fasta {params.dir}/end.fasta | tr -d '\n' >> {output} echo "" >> {output} else grep -v '^>' {params.dir}/$contig.fasta | tr -d '\n' >> {output} echo "" >> {output} fi rm -rf {params.dir}/* done rm -rf {params.dir} else touch {output} fi """ |
332 333 334 335 336 | shell: """ echo {params.random_seed} seqtk sample -s {params.random_seed} {input} {config[number_reads]} > {output} """ |
355 356 357 358 359 360 361 362 | shell: """ samtools view {input.bam} | cut -f1 | sort | uniq > {output.list} seqtk subseq {input.fastFile} {output.list} \ | bioawk -c fastx \ 'length($seq) > {config[read_min_length]} && length($seq) < {config[chloroplast_size]} \ {{print \">\"$name\"\\n\"$seq}}' > {output.fastFile} """ |
405 406 407 408 409 410 | shell: """ awk 'NR == 1 {{print substr($1,2,length($1)), \"0\", \"10000\"}}' {input} > chloro_assembly/reference/index.bed seqtk subseq {input} chloro_assembly/reference/index.bed > {output} rm chloro_assembly/reference/index.bed """ |
A repository to conduct experiments with omnitig-related models for genome assembly. (v0.4.3)
2177 | shell: "${{CONDA_PREFIX}}/bin/time -v seqtk seq -AU '{input.reads}' > '{output.reads}'" |
A pipeline for lightweight screening of Eukaryotic genomes and transcriptomes for recent HGT (v1.0.0)
262 263 264 | shell:''' seqtk subseq {input.fa} {input.gene_lst} > {output} ''' |
Modular Shotgun Sequence Analysis Workflow: Oecophylla - Harnessing Snakemake
334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 | run: aln2ext = {'utree': 'tsv', 'burst': 'b6', 'bowtie2': 'sam'} ext = aln2ext[params['aligner']] with tempfile.TemporaryDirectory(dir=find_local_scratch(TMP_DIR_ROOT)) as temp_dir: shell(""" set +u; {params.env}; set -u # get stem file path stem={output.profile} stem=${{stem%.profile.txt}} # interleave paired fastq's and convert to fasta seqtk mergepe {input.forward} {input.reverse} | \ seqtk seq -A > {temp_dir}/{wildcards.sample}.fna # map reads to reference database shogun align \ --aligner {params.aligner} \ --threads {threads} \ --database {params.db} \ --input {temp_dir}/{wildcards.sample}.fna \ --output {temp_dir} \ 2> {log} 1>&2 # build taxonomic profile based on read map shogun assign_taxonomy \ --aligner {params.aligner} \ --database {params.db} \ --input {temp_dir}/alignment.{params.aligner}.{ext} \ --output {output.profile} \ 2> {log} 1>&2 # keep mapping file if [[ "{params.map}" == "True" ]] then gzip -c {temp_dir}/alignment.{params.aligner}.{ext} > $stem.{params.aligner}.{ext}.gz fi # redistribute reads to given taxonomic ranks if [[ ! -z {params.levels} ]] then IFS=',' read -r -a levels <<< "{params.levels}" for level in "${{levels[@]}}" do shogun redistribute \ --database {params.db} \ --level $level \ --input {output.profile} \ --output $stem.redist.$level.txt \ 2> {log} 1>&2 done fi """) |
HIV Drug Resistance Profiling Pipeline using Bowtie2, Lofreq, and SierraPy
12 13 14 15 16 | shell: """ seqtk trimfq {input.reads1} > {output.trim1} seqtk trimfq {input.reads2} > {output.trim2} """ |
32 33 34 35 36 | shell: """ seqtk sample -s {params.seed} {input.trim1} {params.n} > {output.sub1} seqtk sample -s {params.seed} {input.trim2} {params.n} > {output.sub2} """ |
Repository for the Microbiology Resource Announcements paper on five complete Streptococcus suis genomes
2 | seqtk comp $1 | awk '{gc += ($4 + $5)} {at += ($3 + $6)} END {print gc/(gc + at)}' |
tool / biotools
seqtk
A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip.