Provided by: pilon_1.23+dfsg-1_all
pilon - automated genome assembly improvement and variant detection tool
pilon --genome genome.fasta [--frags frags.bam] [--jumps jumps.bam] [--unpaired unpaired.bam] [...other options...]
Pilon is a software tool which can be used to: · Automatically improve draft assemblies · Find variation among strains, including large event detection Pilon requires as input a FASTA file of the genome along with one or more BAM files of reads aligned to the input FASTA file. Pilon uses read alignment analysis to identify inconsistencies between the input genome and the evidence in the reads. It then attempts to make improvements to the input genome, including: · Single base differences · Small indels · Larger indel or block substitution events · Gap filling · Identification of local misassemblies, including optional opening of new gaps
--help for option details INPUTS --genome genome.fasta The input genome we are trying to improve, which must be the reference used for the bam alignments. At least one of --frags or --jumps must also be given. --frags frags.bam A bam file consisting of fragment paired-end alignments, aligned to the --genome argument using bwa or bowtie2. This argument may be specified more than once. --jumps jumps.bam A bam file consisting of jump (mate pair) paired-end alignments, aligned to the --genome argument using bwa or bowtie2. This argument may be specified more than once. --unpaired unpaired.bam A bam file consisting of unpaired alignments, aligned to the --genome argument using bwa or bowtie2. This argument may be specified more than once. --bam any.bam A bam file of unknown type; Pilon will scan it and attempt to classify it as one of the above bam types. OUTPUTS --output prefix Prefix for output files --outdir directory Use this directory for all output files. --changes If specified, a file listing changes in the <output>.fasta will be generated. --vcf If specified, a vcf file will be generated --vcfqe If specified, the VCF will contain a QE (quality-weighted evidence) field rather than the default QP (quality-weighted percentage of evidence) field. --tracks This options will cause many track files (*.bed, *.wig) suitable for viewing in a genome browser to be written. CONTROL --variant Sets up heuristics for variant calling, as opposed to assembly improvement; equivalent to "--vcf --fix all,breaks". --chunksize Input FASTA elements larger than this will be processed in smaller pieces not to exceed this size (default 10000000). --diploid Sample is from diploid organism; will eventually affect calling of heterozygous SNPs --fix fixlist A comma-separated list of categories of issues to try to fix: "snps": try to fix individual base errors; "indels": try to fix small indels; "gaps": try to fill gaps; "local": try to detect and fix local misassemblies; "all": all of the above (default); "bases": shorthand for "snps" and "indels" (for back compatibility); "none": none of the above; new fasta file will not be written. The following are experimental fix types: "amb": fix ambiguous bases in fasta output (to most likely alternative); "breaks": allow local reassembly to open new gaps (with "local"); "circles": try to close circlar elements when used with long corrected reads; "novel": assemble novel sequence from unaligned non-jump reads. --dumpreads Dump reads for local re-assemblies. --duplicates Use reads marked as duplicates in the input BAMs (ignored by default). --iupac Output IUPAC ambiguous base codes in the output FASTA file when appropriate. --nonpf Use reads which failed sequencer quality filtering (ignored by default). --targets targetlist Only process the specified target(s). Targets are comma-separated, and each target is a fasta element name optionally followed by a base range. Example: "scaffold00001,scaffold00002:10000-20000" would result in processing all of scaffold00001 and coordinates 10000-20000 of scaffold00002. If "targetlist" is the name of a file, each line will be treated as a target specification. --threads Degree of parallelism to use for certain processing (default 1). Experimental. --verbose More verbose output. --debug Debugging output (implies verbose). --version Print version string and exit. HEURISTICS: --defaultqual qual Assumes bases are of this quality if quals are no present in input BAMs (default 15). --flank nbases Controls how much of the well-aligned reads will be used; this many bases at each end of the good reads will be ignored (default 10). --gapmargin Closed gaps must be within this number of bases of true size to be closed (100000) --K Kmer size used by internal assembler (default 47). --mindepth depth Variants (snps and indels) will only be called if there is coverage of good pairs at this depth or more; if this value is >= 1, it is an absolute depth, if it is a fraction < 1, then minimum depth is computed by multiplying this value by the mean coverage for the region, with a minimum value of 5 (default 0.1: min depth to call is 10% of mean coverage or 5, whichever is greater). --mingap Minimum size for unclosed gaps (default 10) --minmq Minimum alignment mapping quality for a read to count in pileups (default 0) --minqual Minimum base quality to consider for pileups (default 0) --nostrays Skip making a pass through the input BAM files to identify stray pairs, that is, those pairs in which both reads are aligned but not marked valid because they have inconsistent orientation or separation. Identifying stray pairs can help fill gaps and assemble larger insertions, especially of repeat content. However, doing so sometimes consumes considerable memory.
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.