Command Line¶
metacov¶
MetaCov estimates abundance values from the stacking depth of reads mapped to a reference.
metacov [OPTIONS] COMMAND [ARGS]...
pileup¶
Compute fold coverage values
metacov pileup [OPTIONS]
Options
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-b,--bamfile<bamfile>¶ Input BAM file. Must be sorted and indexed. [required]
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-f,--reference-fasta<reference_fasta>¶
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-rb,--regionfile-blast7<regionfile_blast7>¶ Input Region file in BLAST7 format
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-rc,--regionfile-csv<regionfile_csv>¶ Input Region file in CSV format
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-k,--kmer-histogram<kmer_histogram>¶ Kmer Histogram produced with metacov scan
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-K,--kmer-length<kmer_length>¶ Length of k-mer
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-o,--outfile<outfile>¶ Output CSV (default STDOUT)
scan¶
Gather read statistics
metacov scan [OPTIONS] READFILE...
Options
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-t,--readfile-type<readfile_type>¶ Override filename based detection of readfile type.
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-m,--max-reads<max_reads>¶ Only consider the first N reads.
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-g,--group-by<group_by>¶ Group output by BAM flag. May be specified multiple times. FLAG can be one of [‘PairedProperly’, ‘MateMapped’, ‘IsRead2’, ‘Readdir’, ‘Paired’, ‘Duplicate’, ‘Alignment’, ‘MateReaddir’, ‘IsRead1’, ‘QC’, ‘Mapped’]
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-f,--reference-fasta<reference_fasta>¶ Fasta file reads where mapped to. Required for boffset. File may be bgzip’ed, but not gzip’ed.
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-b,--out-basehist<out_basehist>¶ Compute histogram of base counts by position in read.
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-bo,--boffset<boffset>¶ Include N bases prior to read start in base histogram. Requires reference fasta file. [default: 0]
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-o,--out-kmerhist<out_kmerhist>¶ Compute histogram of kmers in reads
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-k<k>¶ Length of kmers [default: 7]
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-s,--step<step>¶ Step between sampled kmers [default: 7]
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-O,--offset<offset>¶ Offset of first sampled kmer [default: 0]
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-n,--number<number>¶ Numer of sampled kmers [default: 8]
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-M,--out-mirrorhist<out_mirrorhist>¶ Compute histogram of mismatches against palindrome
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-MO,--mirror-offset<mirror_offset>¶ Offset of palindrome center from read start [default: 4]
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-Ml,--mirror-length<mirror_length>¶ Palindrome length is 2N+1 [default: 10]
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-I,--out-isizehist<out_isizehist>¶ Compute histogram of insert sizes.
Arguments
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READFILE¶ Required argument(s)
simulate¶
Pseudo-Randomly select reads from input file(s).
Input read files may be in SAM, BAM or (gzipped) FastQ format (.sam, .bam, .fq, .fastq, .fq.gz or .fastq.gz).
If a reverse read output filename is provided, input is assumed to be paired reads given either as sam/bam file(s) or pairs of FastQ files.
metacov simulate [OPTIONS] FILE [FILE...]
Options
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-k,--khist<khist>¶ Match distribution of reads to statistics gathered with metacov scan.
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-K,--klen<klen>¶ Length of k-mer
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-p,--proportions<proportions>¶ Specify the proportions in which each genome should occur.
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-o,--out<fwd_outfn>¶ Name of output forward reads fastq file. [required]
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-o2,--out2<rev_outfn>¶ Name of output reverse reads fastq file. [required]
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-n,--num-reads<num_reads>¶ Number of reads to sample
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-rs,--rndSeed<rndseed>¶ Random seed
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-ss,--seqSys<seqsys>¶ Name of Illumina sequencing system
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-l,--len<rlen>¶ Read length
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-m,--mflen<mflen>¶ Mean insert size
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-s,--sdev<sdev>¶ Stddev of insert size
Arguments
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FILE[FILE...]¶ Required argument(s)