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Merge pull request #1076 from Kincekara/bbtools
adds bbtools 39.10
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| FROM staphb/samtools:1.21 as samtools | ||
| FROM staphb/htslib:1.21 as htslib | ||
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| # As a reminder | ||
| # https://github.com/StaPH-B/docker-builds/pull/925#issuecomment-2010553275 | ||
| # bbmap/docs/TableOfContents.txt lists additional dependencies | ||
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| FROM ubuntu:jammy as app | ||
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| ARG SAMBAMBAVER=1.0.1 | ||
| ARG BBTOOLSVER=39.10 | ||
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| LABEL base.image="ubuntu:jammy" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="BBTools" | ||
| LABEL software.version=${BBTOOLSVER} | ||
| LABEL description="A set of tools labeled as \"Bestus Bioinformaticus\"" | ||
| LABEL website="https://sourceforge.net/projects/bbmap" | ||
| LABEL documentation="https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/" | ||
| LABEL license="https://jgi.doe.gov/disclaimer/" | ||
| LABEL maintainer="Abigail Shockey" | ||
| LABEL maintainer.email="[email protected]" | ||
| LABEL maintainer2="Padraic Fanning" | ||
| LABEL maintainer2.email="faninnpm AT miamioh DOT edu" | ||
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| RUN apt-get update && \ | ||
| apt-get install --no-install-recommends -y \ | ||
| openjdk-8-jre-headless \ | ||
| pigz \ | ||
| pbzip2 \ | ||
| lbzip2 \ | ||
| bzip2 \ | ||
| wget \ | ||
| ca-certificates \ | ||
| procps && \ | ||
| rm -rf /var/lib/apt/lists/* && \ | ||
| apt-get autoclean | ||
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| # copy samtools to image | ||
| COPY --from=samtools /usr/local/bin/* /usr/local/bin/ | ||
| COPY --from=htslib /usr/local/bin/* /usr/local/bin/ | ||
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| # download and install sambamba | ||
| RUN wget -q https://github.com/biod/sambamba/releases/download/v${SAMBAMBAVER}/sambamba-${SAMBAMBAVER}-linux-amd64-static.gz && \ | ||
| gzip -d sambamba-${SAMBAMBAVER}-linux-amd64-static.gz && \ | ||
| mv sambamba-${SAMBAMBAVER}-linux-amd64-static /usr/local/bin/sambamba && \ | ||
| chmod +x /usr/local/bin/sambamba | ||
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| # download and install bbtools | ||
| RUN wget -q https://sourceforge.net/projects/bbmap/files/BBMap_${BBTOOLSVER}.tar.gz && \ | ||
| tar -xzf BBMap_${BBTOOLSVER}.tar.gz && \ | ||
| rm BBMap_${BBTOOLSVER}.tar.gz && \ | ||
| mkdir /data | ||
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| ENV PATH=/bbmap/:$PATH \ | ||
| LC_ALL=C | ||
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| CMD tail -n 90 /bbmap/docs/TableOfContents.txt | ||
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| WORKDIR /data | ||
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| # testing | ||
| FROM app as test | ||
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| # get test data and test one thing that uses samtools/sambamba | ||
| RUN wget -q https://raw.githubusercontent.com/StaPH-B/docker-builds/master/tests/SARS-CoV-2/SRR13957123.primertrim.sorted.bam && \ | ||
| streamsam.sh in='SRR13957123.primertrim.sorted.bam' out='test_SRR13957123.primertrim.sorted.fastq.gz' && \ | ||
| test -f test_SRR13957123.primertrim.sorted.fastq.gz |
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| # BBTools container | ||
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| Main tool: [BBTools](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/) | ||
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| Code repository: https://sourceforge.net/projects/bbmap/ | ||
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| Additional tools: | ||
| - samtools: 1.21 | ||
| - htslib: 1.21 | ||
| - sambamba: 1.0.1 | ||
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| Basic information on how to use this tool: | ||
| - executable: *.sh | ||
| - help: Program descriptions and options are shown when running the shell scripts with no parameters. | ||
| - version: --version | ||
| - description: | ||
| >BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data. BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw, with autodetection of quality encoding and interleaving. | ||
| Additional information: | ||
| | Script | Purpose | Comment | | ||
| |-------------------------|----------------------------------------------------------------------------------|------------------------------------------------------------------------| | ||
| | bbcms.sh | Performs error correction using a Count-Min Sketch | Intended for metagenome assembly assembly | | ||
| | bbcountunique.sh | Counts unique kmers in reads | | | ||
| | bbduk.sh | Trims, filters or masks reads using kmers | | | ||
| | bbmap.sh | Splice-aware aligner for short reads | | | ||
| | bbmapskimmer.sh | BBMap version designed for high levels of multimapping | | | ||
| | bbmask.sh | Masks references based on various things, such as sequence complexity | | | ||
| | bbmerge.sh | Merges overlapping paired reads | | | ||
| | bbmerge-auto.sh | Same as bbmerge, but tries to allocate all memory on the node | Use this version for kmer operations like extend | | ||
| | bbnorm.sh | Normalizes reads based on coverage | Mainly for use prior to single-cell assembly | | ||
| | bbsplit.sh | BBMap version that maps to multiple references simultaneously | Intended for decontamination; similar to Seal | | ||
| | bbversion.sh | Prints the version of BBTools | | | ||
| | bbwrap.sh | Wraps BBMap to process many files using same reference | Saves time by loading the index only once | | ||
| | calctruequality.sh | Allows recalibration of quality scores from mapped reads | This generates the correction matrix; BBDuk does the recalibration | | ||
| | callgenes.sh | Fast prokaryotic gene caller | Integrated into BBSketch | | ||
| | callvariants.sh | Fast variant caller | | | ||
| | callvariants2.sh | Same as callvariants.sh with the "multisample" flag | | | ||
| | clumpify.sh | Shrinks compressed fastq files, and can remove duplicate reads | Also supports error correction | | ||
| | comparesketch.sh | Compares sketches locally, without using a sketch server | | | ||
| | crossblock.sh | Alias for decontaminate.sh | | | ||
| | cutgff.sh | Cuts out features defined by gff file | E.g, generates one fasta entry per gene from a gff and an assembly | | ||
| | cutprimers.sh | Cuts out subregions of ribosomes | Mainly for 16S analysis | | ||
| | decontaminate.sh | Pool-level decontamination for single-cell MDA-amplified genomes | | | ||
| | dedupe.sh | Removes duplicate and fully-contained sequences | Can also be used to cluster 16S sequences | | ||
| | dedupe2.sh | Version of dedupe that supports more hash keys for greater sensitivity | | | ||
| | dedupebymapping.sh | Deduplicates reads based on mapping coordinates | | | ||
| | demuxbyname.sh | Demultiplexes based on sequences headers | | | ||
| | filterbyname.sh | Filters based on sequence headers | | | ||
| | filterbytaxa.sh | Filters sequences based on taxonomic classification | Used with NCBI datasets | | ||
| | filterbytile.sh | Removes reads that are in low quality areas on flowcell | | | ||
| | filterqc.sh | Part of JGI's fastq filtering pipeline | | | ||
| | filtersam.sh | Filters sam files to remove reads with multiple unsupported mismatches | Designed for NovaSeq | | ||
| | gitable.sh | Used to process NCBI taxonomy data | | | ||
| | khist.sh | Alias for bbnorm.sh with flags for making a kmer frequency histogram | | | ||
| | kmercountexact.sh | Counts kmers and produces a histogram | Uses more memory than BBNorm but allows exact counts | | ||
| | kmercountmulti.sh | Cardinality estimation over multiple kmer lengths | Uses LogLog; does not produce a histogram | | ||
| | mapPacBio.sh | BBMap version designed for PacBio or Nanopore reads | Reads longer than 5kbp get broken into 5kbp shreds | | ||
| | mergesketch.sh | Allows multiple sketches to be combined | | | ||
| | msa.sh | Alignment tool | Used with cutprimers.sh to cut subsections out of 16s | | ||
| | mutate.sh | Generates synthetic genomes by randomly mutating the input | | | ||
| | muxbyname.sh | Multiplex multiple files, renaming sequences based on input file name | Opposite of demuxbyname.sh | | ||
| | partition.sh | Splits a sequence file into multiple files | | | ||
| | pileup.sh | Calculates coverage from sam files | | | ||
| | plotflowcell.sh | Produces statistics about flowcell positions | | | ||
| | processhi-c.sh | Custom trimming for hi-C reads | In development | | ||
| | randomreads.sh | Generates synthetic data from real genome reference | Highly customizable | | ||
| | readqc.sh | Short read quality report | Alternative to fastqc | | ||
| | reformat.sh | Converts sequence files to another format | Has many additional options, includes subsampling | | ||
| | rename.sh | Renames sequences in various ways, such as adding a prefix | | | ||
| | repair.sh | Fixes broken pairing in fastq files | | | ||
| | representative.sh | Makes a smaller subset of a reference dataset by eliminating redundancy | Designed for use with BBSketch output | | ||
| | rqcfilter2.sh | Filtering pipeline used at JGI | portal.nersc.gov/dna/microbial/assembly/bushnell/RQCFilterData.tar | | ||
| | seal.sh | Counts kmer matches between query and reference sequences | | | ||
| | sendsketch.sh | Fast taxonomic classifier using webservers at JGI | | | ||
| | shred.sh | Breaks sequences into shorter, fixed-length pieces | | | ||
| | shuffle.sh | Randomly reorders input file | Crashes if input doesn't fit in memory | | ||
| | shuffle2.sh | Randomly reorders input file | Supports larger files, but output might be less random | | ||
| | sketch.sh | Makes reference sketches on a per-TaxID basis | | | ||
| | sketchblacklist.sh | Makes sketch blacklists of common kmers | | | ||
| | sortbyname.sh | Sorts sequences by name, length, quality, taxa, and other things | | | ||
| | summarizequast.sh | Generates box plots for multiple quast reports | | | ||
| | tadpipe.sh | Preprocessing and assembly pipeline using tadpole | | | ||
| | tadpole.sh | Fast short read assembler | | | ||
| | tadwrapper.sh | Runs Tadpole with multiple kmer lengths to select the best assembly | | | ||
| | taxserver.sh | Starts taxonomy and sketch servers | | | ||
| | testformat.sh | Determines if file is fasta, fastq, interleaved, etc. by reading first few lines | | | ||
| | testformat2.sh | Generates extensive statistics by reading the full file | | | ||
| | translate6frames.sh | Translates nucleotide sequence into amino acid sequence in all frames | | | ||
| | vcf2gff.sh | Converts vcf format to gff format | | | ||
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| Full documentation: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/ | ||
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| ## Example Usage | ||
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| (adapted from `/opt/bbmap/pipelines/covid/processCorona.sh`) | ||
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| Interleave a pair of FASTQ files for downstream processing: | ||
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| ```text | ||
| reformat.sh \ | ||
| in1=${SAMPLE}_R1.fastq.gz \ | ||
| in2=${SAMPLE}_R2.fastq.gz \ | ||
| out=${SAMPLE}.fastq.gz | ||
| ``` | ||
| Split into SARS-CoV-2 and non-SARS-CoV-2 reads: | ||
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| ```text | ||
| bbduk.sh ow -Xmx1g \ | ||
| in=${SAMPLE}.fq.gz \ | ||
| ref=REFERENCE.fasta \ | ||
| outm=${SAMPLE}_viral.fq.gz \ | ||
| outu=${SAMPLE}_nonviral.fq.gz \ | ||
| k=25 | ||
| ``` |