There is a pipeline for calling eccDNA based on this software and singularity, please see panxiaoguang/Circle-Map-Cpp_Pipeline
Circle-Map is a great tool to detect thousands of extrachromosomal circular DNA (eccDNA). Thanks to this tool, we can easily get eccDNA from Circle-Seq data!
But Circle-map realigner has low performance because it uses Python. It also has some errors in the result, especially at the start site, which will incorrectly add 1 bp.
So we used C++ to rewrite Realiger and also corrected all the errors in its result! Welcome to try and give me some suggestion!
see https://github.com/iprada/Circle-Map and https://github.com/BGI-Qingdao/Circle-Map for details.
- c++ std11 compiler environment
- g++
- make
- htslib
- zlib
- bzip2
- xz
- python3 with libraries
- pysam
- argparse
- numpy
- bedtools
conda install -c bioconda circle-map-cpp
Or install from source codes:
For how to build an image or other details, please see panxiaoguang/Singularity_CircleMapPlus
wget https://github.com/panxiaoguang/Singularity_CircleMapPlus/releases/download/0.0.5/panxiaoguang-Singularity_CircleMapPlus.latest.sifhow to use?
If you already have a singularity program, just need to
## for readExtractor
singularity exec panxiaoguang-Singularity_CircleMapPlus.latest.sif circle_map++ ReadExtractor -i qname_unknown_circle.bam -o circular_read_candidates.bam
## for realign
singularity exec --bind /home/panxiaoguang/Genome/hg38_bwa/:/hg38_bwa panxiaoguang-Singularity_CircleMapPlus.latest.sif circle_map++ Realign -i sort_circular_read_candidates.bam -qbam qname_unknown_circle.bam -sbam sorted_unknown_circle.bam -fasta /hg38_bwa/hg38.fa -o my_unknown_circle.bed
## for more paramaters
singularity exec panxiaoguang-Singularity_CircleMapPlus.latest.sif circle_map++ --helpNote you should use --bind to bind a local dir into img dir
If you don't have a singularity program, you can install it or using conda version.
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you should firstly compile htslib according to this instructions : Install
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then add the htslib to your $ENV like this:
export C_INCLUDE_PATH="your htslib path/include":$C_INCLUDE_PATH
export CPLUS_INCLUDE_PATH="your htslib path/include":$CPLUS_INCLUDE_PATH
export LIBRARY_PATH="your htslib path/lib":$LIBRARY_PATH
export LD_LIBRARY_PATH="your htslib path/lib":$LD_LIBRARY_PATH- next, make file
make- the prior pipeline will compile
realign_cm.cpp,merge_result.cppandedlib
Please take note of your RAM! we load all the IO files created by the original Circle-Map into the RAM, we will use more RAM than the Circle-Map. Actually, if you have a deep sequencing of circle-seq, you will use more than 70 GB of RAM!
Usage: circle_map++ <subprogram> [options]
Commands:
ReadExtractor Extract circular DNA read candidates
Realign Realign circular DNA read candidates
usage: circle_map++ ReadExtractor [options]
Extracts circular DNA read candidates
required arguments:
-i Input: query name sorted bam file
optional arguments:
-o , --output Output: Reads indicating circular DNA structural variants
-t , --threads Number of threads to use. Default 1
-dir , --directory Working directory, default is current working directory
-q , --quality bwa-mem mapping quality cutoff. Default value 10
-nd, --nodiscordant Turn off discordant (R2F1 oriented) read extraction
-nsc, --nosoftclipped
Turn off soft-clipped read extraction
-nhc, --nohardclipped
Turn off hard-clipped read extraction
-v , --verbose Verbose level, 1=error,2=warning, 3=message
usage: circle_map++ Realign [options]
Realign circular DNA read candidates
Input/Output options:
-i Input: bam file containing reads extracted by ReadExtractor
-qbam Input: query name sorted bam file
-sbam Input: coordinate sorted bam file
-fasta Input: Reference genome fasta file
-o , --output Output filename
Running options:
-t , --threads Number of threads to use. Default 1
-dir , --directory Working directory, default will create a tmp_${pid} folder in the current working directory and automatically delete it when exit.
-N, --no_coverage Don't compute coverage statistics
Candidate intervals:
-K , --clustering_dist
Cluster reads that are K nucleotides apart in the same node. Default: 500
Insert size estimation options:
-ss , --sample_size Number of concordant reads (R2F1) to use for estimating the insert size distribution. Default 100000
-iq , --insert_mapq Mapq cutoff for estimating the insert size distribution. Default 60
Interval processing options:
-m , --mean_is_size mean value of insert size
-di , --sd_val_insert
SD Value of insert size
-S , --std_factor std_factor, extern realign interval by mIS+sIS*std_factor.(default 4)
-q , --mapping_qual minimum mapping quality (default 20)
-p , --min_interval_prob
minimum interval probability (default 0.01)
-e , --edit_dist_fraction
edit distance fraction (default 0.05)
-l , --min_softclip_len
minimum softclip length (default 8)
-rn , --max_aln_num nhit, maximum alignment number(default 10)
-G , --penity_gap_open
penalty for gap open (default 5)
-E , --penity_gap_extern
penalty for gap extern (default 1)
-P , --aln_prob alignment probability (default 0.99)
Merge result options:
-f , --merge_fraction
Merge intervals reciprocally overlapping by a fraction. Default 0.99
-af , --allele_frequency
Minimum allele frequency required to report the circle interval. Default (0.1)
-O , --number_of_discordants
Number of required discordant reads for intervals with only discordants. Default: 3
-T , --split Number of required split reads to output an eccDNA. Default: 0
-Q , --split_quality
Minimum split score to output an interval. Default (0.0)
-bs , --bases Number of bases to extend for computing the coverage ratio. Default: 200
-ce , --extension Number of bases inside the eccDNA breakpoint coordinates to compute the ratio. Default: 100
-r , --ratio Minimum in/out required coverage ratio. Default: 0.0