Commit dc5bbee2 authored by Raphael Müller's avatar Raphael Müller
Browse files

updated readme

parent 5ff69f92
......@@ -25,71 +25,74 @@ conda activate backmap
## Usage
```
backmap v0.4
backmap v0.5
Description:
Automatic mapping of paired, unpaired, PacBio and Nanopore reads to an
assembly, execution of qualimap bamqc, multiqc and estimation of genome size
from mapped nucleotides and peak coverage.
With the provided conda environment configuration file (environment.yml),
a conda environment with all necessary tools can be created.
Automatic mapping of paired, unpaired, PacBio and Nanopore reads to an
assembly, execution of qualimap bamqc, multiqc and estimation of genome size
from mapped nucleotides and peak coverage.
With the provided conda environment configuration file (environment.yml),
a conda environment with all necessary tools can be created.
Be aware that this pipeline was transferred to a nextflow pipeline with major
changes to version v0.3.
Be aware that this pipeline was transferred to a nextflow pipeline with major
changes from version v0.3 to v.0.4.
Usage:
With mapping:
nextflow run backmap.nf --assembly assembly.fa
[--single-end <unpaired.fq>[,unpaired2.fq,...]]
[--paired-end <paired1.1.fq>,<paired1.2.fq>[,<paired2.1.fq>,<paired2.2.fq>,...]]
[--pacbio <pacbio.fq>[,<pacbio2.fq>,...]]
[--nanopore <nanopore.fq>[,<nanopore2.fq>,...]]
Without mapping:
nextflow run backmap.nf [--assembly assembly.fa]
[--illumina-bam-files illumina.bam[,illumina2.bam,...]]
[--pacbio-bam-files pacbio.bam[,pacbio2.bam,...]]
[--nanopore-bam-files nanopore.bam[,nanopore2.bam,...]]
With mapping:
nextflow run backmap.nf --assembly assembly.fa
[--single-end <unpaired.fq>[,unpaired2.fq,...]]
[--paired-end <paired1.1.fq>,<paired1.2.fq>[,<paired2.1.fq>,<paired2.2.fq>,...]]
[--pacbio <pacbio.fq>[,<pacbio2.fq>,...]]
[--pacbio-ccs <pacbio_ccs.fq>[,<pacbio_ccs2.fq>,...]]
[--nanopore <nanopore.fq>[,<nanopore2.fq>,...]]
Without mapping:
nextflow run backmap.nf [--assembly assembly.fa]
[--illumina-bam-files illumina.bam[,illumina2.bam,...]]
[--pacbio-bam-files pacbio.bam[,pacbio2.bam,...]]
[--pacbio-ccs-bam-files pacbio_ccs.bam[,pacbio_ccs2.bam,...]]
[--nanopore-bam-files nanopore.bam[,nanopore2.bam,...]]
Mandatory options:
--assembly STR Assembly were reads should mapped to in fasta format
AND AT LEAST ONE OF
--single-end STR Fastq files with unpaired Illumina reads, comma separated
--paired-end STR Two fastq files with paired Illumina reads, comma separated
--pacbio STR Fasta or fastq file with PacBio reads, comma separated
--nanopore STR Fasta or fastq file with Nanopore reads, comma separated
OR
--illumina-bam-files STR Premapped Illumina Reads in bam format, comma separated
--pacbio-bam-files STR Premapped Pacbio Reads in bam format, comma separated
--nanopore-bam-files STR Premapped Nanopore Reads in bam format, comma separated
Skips read mapping
Genome size estimation only possible if assembly is given
--assembly STR Assembly were reads should mapped to in fasta format
AND AT LEAST ONE OF
--single-end STR Fastq files with unpaired Illumina reads, comma separated
--paired-end STR Two fastq files with paired Illumina reads, comma separated
--pacbio STR Fasta or fastq file with PacBio reads (CLR), comma separated
--pacbio-ccs STR Fasta or fastq file with PacBio CCS reads, comma separated
--nanopore STR Fasta or fastq file with Nanopore reads, comma separated
OR
--illumina-bam-files STR Premapped Illumina Reads in bam format, comma separated
--pacbio-bam-files STR Premapped Pacbio Reads in bam format, comma separated
--pacbio-ccs-bam-files STR Premapped Pacbio CCS Reads in bam formac, comma separated
--nanopore-bam-files STR Premapped Nanopore Reads in bam format, comma separated
Skips read mapping
Genome size estimation only possible if assembly is given
Optional Options: [default]
--file-separator STR Overrides file separator [,]
--output STR Output directory [./Results/]
Will be created if not existing
--prefix STR Prefix of output files [tbg_backmap]
--keep-temporary Keep temporary, intermediate files [false]
--threads INT Maximum number of threads per process [1]
This is not the total number of available threads!
--skip-quality-control Skip qualimap bamqc run [false]
--skip-coverage-histogram Skip creation of coverage histograms [false]
--skip-genome-size-estimation Skip genome size estimation [false]
genome size estimation is only possible, if assembly is given
--bwa-options STR Options passed to bwa [-a -c 10000]
--minimap-pacbio-options STR Options passed to minimap ["-H"]
--minimap-nanopore-options STR Options passes to nanopore minimap runs [""]
--qualimap-options STR Options passed to qualimap [""]
Pass options with quotes e.g. --bwa-options "<options>"
--help Print this help and exit
--version Print version number and exit
--debug Print inner variables
--file-separator STR Overrides file separator [,]
--output STR Output directory [./Results/]
Will be created if not existing
--prefix STR Prefix of output files [tbg_backmap]
--keep-temporary Keep temporary, intermediate files [false]
--threads INT Maximum number of threads per process [1]
This is not the total number of available threads!
--skip-quality-control Skip qualimap bamqc run [false]
--skip-coverage-histogram Skip creation of coverage histograms [false]
--skip-genome-size-estimation Skip genome size estimation [false]
genome size estimation is only possible, if assembly is given
--bwa-options STR Options passed to bwa [-a -c 10000]
--minimap-pacbio-options STR Options passed to pacbio CLR minimap runs ["-H"]
--minimap-pacbio-ccs-options STR Options passed to pacbio CCS minimap runs [""]
--minimap-nanopore-options STR Options passes to nanopore minimap runs [""]
--qualimap-options STR Options passed to qualimap [""]
Pass options with quotes e.g. --bwa-options "<options>"
--help Print this help and exit
--version Print version number and exit
--debug Print inner variables
```
......@@ -99,6 +102,7 @@ Optional Options: [default]
graph TD;
Assembly[[Assembly]] --> BWAIndex{bwa index};
Assembly --> MinimapP{minimap2};
Assembly --> MinimapPCCS{minimap2};
Assembly --> MinimapN{minimap2};
BWAI --> BWAMemSE{bwa mem};
BWAI --> BWAMemPE{bwa mem};
......@@ -114,10 +118,14 @@ graph TD;
end
subgraph PacBio
PB[[PacBio Reads]] --> MinimapP;
PB[[PacBio CLR Reads]] --> MinimapP;
PBCCS[[PacBio CCS Reads]] --> MinimapPCCS;
MinimapP --> MBam[[Pacbio Mapped Reads]] --> SMP{samtools merge};
MinimapPCCS --> MPCCSBam[[Pacbio CCS Mapped Reads]] --> SMPCCS{samtools merge};
SMP --> PMer[Pacbio Merged Bam Files] --> SSP{samtools sort};
SMPCCS --> PCCSMer[Pacbio CCS Merged Bam Files] --> SSPCCS{samtools sort};
SSP --> PSor[Pacbio Sorted Bam Files];
SSPCCS --> PCCSSor[Pacbio CCS Sorted Bam Files];
end
subgraph Nanopore
......@@ -129,17 +137,20 @@ graph TD;
ISor --> QMI{qualimap} --> MultiQC{{multiqc}}
PSor --> QMI
PCCSSor --> QMI
NSor --> QMI
ISor --> bedI{bedtools genomecov} --> RCovSingleI{{"R Coverage Plot (single)"}}
PSor --> bedI
PCCSSor --> bedI
NSor --> bedI
bedI --> RCovMulti{{"R Coverage Plot (multi)"}}
ISor --> SSTI{{samtools stat}}
PSor --> SSTI
PCCSSor --> SSTI
NSor --> SSTI
bedI --> GSEI{{Genome Size Estimation}}
......@@ -153,6 +164,7 @@ graph TD;
- {+ all options now have a long version, short version is currently not available +}
- {+ added option \`--illumina-bam-files\`, \`--pacbio-bam-files\`, \`--nanopore-bam-files\`, which substitute \`-b\` +}
- {+ added option \`--pacbio-ccs-bam-files\`, \`--pacbio-ccs\` +}
- {+ \`--debug\` prints internal variables for faster development and bug investigations +}
- {+ \`--threads\` sets the maximum number of threads per process (not maximum number of threads of the whole workflow) +}
- {- removed \`-b\`:splitted into three different options -}
......
......@@ -23,12 +23,14 @@ Usage:
[--single-end <unpaired.fq>[,unpaired2.fq,...]]
[--paired-end <paired1.1.fq>,<paired1.2.fq>[,<paired2.1.fq>,<paired2.2.fq>,...]]
[--pacbio <pacbio.fq>[,<pacbio2.fq>,...]]
[--pacbio-ccs <pacbio_ccs.fq>[,<pacbio_ccs2.fq>,...]]
[--nanopore <nanopore.fq>[,<nanopore2.fq>,...]]
Without mapping:
nextflow run backmap.nf [--assembly assembly.fa]
[--illumina-bam-files illumina.bam[,illumina2.bam,...]]
[--pacbio-bam-files pacbio.bam[,pacbio2.bam,...]]
[--pacbio-ccs-bam-files pacbio_ccs.bam[,pacbio_ccs2.bam,...]]
[--nanopore-bam-files nanopore.bam[,nanopore2.bam,...]]
Mandatory options:
......
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