abnerchang/arcs repository overview

/ARCS/PATH/bin/arcs --help arcs 1.0.1 Usage: arcs [OPTION]... -f FASTA_FILE BAM_FILE...

NOTE 1: BAM_FILE must be sorted in order of name NOTE 2: read names in BAM_FILE must be formatted as <READ_NAME>_<BARCODE_SEQ>

Options: -f, --file=FILE input sequences to scaffold [required] -a, --fofName=FILE text file listing input BAM filenames -s, --seq_id=N min sequence identity for read alignments [98] -c, --min_reads=N min aligned read pairs per barcode mapping [5] -l, --min_links=N min shared barcodes between contigs [0] -z, --min_size=N min contig length [500] -b, --base_name=STR output file prefix -g, --graph=FILE write the ABySS dist.gv to FILE --gap=N fixed gap size for ABySS dist.gv file [100] --tsv=FILE write graph in TSV format to FILE --barcode-counts=FILE write number of reads per barcode to FILE -m, --index_multiplicity=RANGE barcode multiplicity range [50-10000] -d, --max_degree=N max node degree in scaffold graph [0] -e, --end_length=N contig head/tail length for masking alignments [30000] -r, --error_percent=N p-value for head/tail assignment and link orientation (lower is more stringent) [0.05] -v, --run_verbose verbose logging

Distance Estimation Options:

-B, --bin_size=N estimate distance using N closest Jaccard scores [20] -D, --dist_est enable distance estimation --no_dist_est disable distance estimation [default] --dist_median use median distance in ABySS dist.gv [default] --dist_upper use upper bound distance in ABySS dist.gv --dist_tsv=FILE write min/max distance estimates to FILE --samples_tsv=FILE write intra-contig distance/barcode samples to FILE

See details in /ngs/arcs-master/

LINKS 1,8.5 in /ngs/links_v1.8.5