From 94abf2215fa00e8ce5fd98bdbe9a1a686625d37b Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Fri, 11 Dec 2020 07:34:13 +1000 Subject: [PATCH] v0.6.0 --- Cargo.toml | 2 +- docs/coverm-cluster.html | 4 ++-- docs/coverm-contig.html | 33 ++++++++++++++++++++++++++++++--- docs/coverm-filter.html | 23 ++++++++++++++++++++--- docs/coverm-genome.html | 36 +++++++++++++++++++++++++++++++++--- docs/coverm-make.html | 20 +++++++++++++++++--- 6 files changed, 103 insertions(+), 15 deletions(-) diff --git a/Cargo.toml b/Cargo.toml index 04c05c3..f8241e7 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -1,6 +1,6 @@ [package] name = "coverm" -version = "0.5.0" +version = "0.6.0" authors = ["Ben Woodcroft "] license = "GPL-3.0" description = "Read coverage calculator for metagenomics" diff --git a/docs/coverm-cluster.html b/docs/coverm-cluster.html index 698e81b..7f38e68 100644 --- a/docs/coverm-cluster.html +++ b/docs/coverm-cluster.html @@ -63,7 +63,7 @@
coverm cluster usage Ben Woodcroft, Centre for Microbiome Research, Queensland University of Technology -2020-08-28 (coverm 0.5.0) +2020-12-11 (coverm 0.6.0)
@@ -90,7 +90,7 @@

NAME

-

coverm cluster - Cluster genome FASTA files by average nucleotide identity (version 0.5.0)

+

coverm cluster - Cluster genome FASTA files by average nucleotide identity (version 0.6.0)

SYNOPSIS

diff --git a/docs/coverm-contig.html b/docs/coverm-contig.html index b05706a..a2289d1 100644 --- a/docs/coverm-contig.html +++ b/docs/coverm-contig.html @@ -63,7 +63,7 @@
coverm contig usage Ben Woodcroft, Centre for Microbiome Research, Queensland University of Technology -2020-08-28 (coverm 0.5.0) +2020-12-11 (coverm 0.6.0)
@@ -84,7 +84,9 @@
  • COVERAGE CALCULATION OPTIONS
  • OUTPUT
  • GENERAL OPTIONS
    • +
  • FREQUENTLY ASKED QUESTIONS
  • EXIT STATUS
    • +
  • EXAMPLES
  • AUTHOR
    • @@ -93,7 +95,7 @@

    NAME

    -

    coverm contig - Calculate read coverage per-contig (version 0.5.0)

    +

    coverm contig - Calculate read coverage per-contig (version 0.6.0)

    SYNOPSIS

    @@ -313,6 +315,10 @@

    COVERAGE CALCULATION OPTIONS

    rpkm Reads mapped per kilobase of contig, per million mapped reads + +tpm +Transcripts Per Million as described in Li et al 2010 https://doi.org/10.1093/bioinformatics/btp692 +
    @@ -342,6 +348,12 @@

    COVERAGE CALCULATION OPTIONS

    OUTPUT

    +
    o, --output-file FILE
    +

    Output coverage values to this file, or '-' for STDOUT. [default: output to STDOUT]

    +
    +
    + +
    --output-format FORMAT

    Shape of output: 'sparse' for long format, 'dense' for species-by-site. [default: dense]

    @@ -403,6 +415,10 @@

    GENERAL OPTIONS

    +
    +

    FREQUENTLY ASKED QUESTIONS

    +

    Can the temporary directory used be changed? CoverM makes use of the system temporary directory (often /tmp) to store intermediate files. This can cause problems if the amount of storage available there is small or used by many programs. To fix, set the TMPDIR environment variable e.g. to set it to use the current directory: TMPDIR=. coverm genome <etc>

    +

    EXIT STATUS

    @@ -423,10 +439,21 @@

    EXIT STATUS

    +
    +

    EXAMPLES

    +
    +
    Calculate mean coverage from reads and assembly
    +

    $ coverm contig --coupled read1.fastq.gz read2.fastq.gz --reference assembly.fna

    +
    +
    Calculate MetaBAT adjusted coverage from a sorted BAM file, saving the unfiltered BAM files in the saved_bam_files folder
    +

    $ coverm contig --method metabat --bam-files my.bam --bam-file-cache-directory saved_bam_files

    +
    +
    +

    AUTHOR

    -
    Ben J. Woodcroft, Centre for Microbiome Research, Queensland University of Technology <benjwoodcroft near gmail.com>
    +
    Ben J. Woodcroft, Centre for Microbiome Research, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology <benjwoodcroft near gmail.com>
    diff --git a/docs/coverm-filter.html b/docs/coverm-filter.html index 014bcca..357a86e 100644 --- a/docs/coverm-filter.html +++ b/docs/coverm-filter.html @@ -63,7 +63,7 @@
    coverm filter usage Ben Woodcroft, Centre for Microbiome Research, Queensland University of Technology -2020-08-28 (coverm 0.5.0) +2020-12-11 (coverm 0.6.0)
    @@ -79,7 +79,9 @@
  • FLAGS
  • OPTIONS
  • ALIGNMENT THRESHOLDING
    • +
  • FREQUENTLY ASKED QUESTIONS
  • EXIT STATUS
    • +
  • EXAMPLES
  • AUTHOR
    • @@ -88,7 +90,7 @@

    NAME

    -

    coverm filter - Threshold alignments with insufficient identity (version 0.5.0)

    +

    coverm filter - Threshold alignments with insufficient identity (version 0.6.0)

    SYNOPSIS

    @@ -206,6 +208,10 @@

    ALIGNMENT THRESHOLDING

    +
    +

    FREQUENTLY ASKED QUESTIONS

    +

    Can the temporary directory used be changed? CoverM makes use of the system temporary directory (often /tmp) to store intermediate files. This can cause problems if the amount of storage available there is small or used by many programs. To fix, set the TMPDIR environment variable e.g. to set it to use the current directory: TMPDIR=. coverm genome <etc>

    +

    EXIT STATUS

    @@ -226,10 +232,21 @@

    EXIT STATUS

    +
    +

    EXAMPLES

    +
    +
    Filter a BAM file by removing alignments shorter than 50bp
    +

    $ coverm filter --bam-files input.bam --output-bam filtered.bam --min-read-aligned-length 50

    +
    +
    Filter inverse: Keep alignments that have <95% alignment identity and those which do map at all. Note that the output BAM file will likely records that are still mapped, but align with < 95% identity. Use 16 threads for output compression
    +

    $ coverm filter -b input.bam -o inverse_filtered.bam --inverse --min-read-percent-identity 0.95 --threads 16

    +
    +
    +

    AUTHOR

    -
    Ben J. Woodcroft, Centre for Microbiome Research, Queensland University of Technology <benjwoodcroft near gmail.com>
    +
    Ben J. Woodcroft, Centre for Microbiome Research, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology <benjwoodcroft near gmail.com>
    diff --git a/docs/coverm-genome.html b/docs/coverm-genome.html index 4243a49..0ecdddf 100644 --- a/docs/coverm-genome.html +++ b/docs/coverm-genome.html @@ -63,7 +63,7 @@
    coverm genome usage Ben Woodcroft, Centre for Microbiome Research, Queensland University of Technology -2020-08-28 (coverm 0.5.0) +2020-12-11 (coverm 0.6.0)
    @@ -85,7 +85,9 @@
  • COVERAGE CALCULATION OPTIONS
  • OUTPUT
  • GENERAL OPTIONS
    • +
  • FREQUENTLY ASKED QUESTIONS
  • EXIT STATUS
    • +
  • EXAMPLES
  • AUTHOR
    • @@ -94,7 +96,7 @@

    NAME

    -

    coverm genome - Calculate read coverage per-genome (version 0.5.0)

    +

    coverm genome - Calculate read coverage per-genome (version 0.6.0)

    SYNOPSIS

    @@ -476,6 +478,10 @@

    COVERAGE CALCULATION OPTIONS

    rpkm Reads mapped per kilobase of genome, per million mapped reads + +tpm +Transcripts Per Million as described in Li et al 2010 https://doi.org/10.1093/bioinformatics/btp692 +
    @@ -505,6 +511,12 @@

    COVERAGE CALCULATION OPTIONS

    OUTPUT

    +
    o, --output-file FILE
    +

    Output coverage values to this file, or '-' for STDOUT. [default: output to STDOUT]

    +
    +
    + +
    --output-format FORMAT

    Shape of output: 'sparse' for long format, 'dense' for species-by-site. [default: dense]

    @@ -566,6 +578,10 @@

    GENERAL OPTIONS

    +
    +

    FREQUENTLY ASKED QUESTIONS

    +

    Can the temporary directory used be changed? CoverM makes use of the system temporary directory (often /tmp) to store intermediate files. This can cause problems if the amount of storage available there is small or used by many programs. To fix, set the TMPDIR environment variable e.g. to set it to use the current directory: TMPDIR=. coverm genome <etc>

    +

    EXIT STATUS

    @@ -586,10 +602,24 @@

    EXIT STATUS

    +
    +

    EXAMPLES

    +
    +
    Map paired reads to 2 genomes, and output relative abundances to output.tsv
    +

    $ coverm genome --coupled read1.fastq.gz read2.fastq.gz --genome-fasta-files genome1.fna genome2.fna -o output.tsv

    +
    +
    Calculate coverage of genomes defined as .fna files in genomes_directory/ from a sorted BAM file
    +

    $ coverm genome --bam-files my.bam --genome-fasta-directory genomes_directory/

    +
    +
    Dereplicate genomes at 99% ANI before mapping unpaired reads
    +

    $ coverm genome --genome-fasta-directory genomes/ --dereplicate --single single_reads.fq.gz

    +
    +
    +

    AUTHOR

    -
    Ben J. Woodcroft, Centre for Microbiome Research, Queensland University of Technology <benjwoodcroft near gmail.com>
    +
    Ben J. Woodcroft, Centre for Microbiome Research, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology <benjwoodcroft near gmail.com>
    diff --git a/docs/coverm-make.html b/docs/coverm-make.html index b1be786..b86d98b 100644 --- a/docs/coverm-make.html +++ b/docs/coverm-make.html @@ -63,7 +63,7 @@
    coverm make usage Ben Woodcroft, Centre for Microbiome Research, Queensland University of Technology -2020-08-28 (coverm 0.5.0) +2020-12-11 (coverm 0.6.0)
    @@ -81,7 +81,9 @@
  • MAPPING ALGORITHM OPTIONS
  • OUTPUT
  • GENERAL OPTIONS
    • +
  • FREQUENTLY ASKED QUESTIONS
  • EXIT STATUS
    • +
  • EXAMPLES
  • AUTHOR
    • @@ -90,7 +92,7 @@

    NAME

    -

    coverm make - Generate BAM files through mapping (version: 0.5.0)

    +

    coverm make - Generate BAM files through mapping (version: 0.6.0)

    SYNOPSIS

    @@ -244,6 +246,10 @@

    GENERAL OPTIONS

    +
    +

    FREQUENTLY ASKED QUESTIONS

    +

    Can the temporary directory used be changed? CoverM makes use of the system temporary directory (often /tmp) to store intermediate files. This can cause problems if the amount of storage available there is small or used by many programs. To fix, set the TMPDIR environment variable e.g. to set it to use the current directory: TMPDIR=. coverm genome <etc>

    +

    EXIT STATUS

    @@ -264,10 +270,18 @@

    EXIT STATUS

    +
    +

    EXAMPLES

    +
    +
    Map pair of read files to the combined_genomes.fna reference, storing sorted BAM files in output_dir/
    +

    $ coverm make -r combined_genomes.fna -1 read1.fq -2 read2.fq -o output_dir

    +
    +
    +

    AUTHOR

    -
    Ben J. Woodcroft, Centre for Microbiome Research, Queensland University of Technology <benjwoodcroft near gmail.com>
    +
    Ben J. Woodcroft, Centre for Microbiome Research, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology <benjwoodcroft near gmail.com>