usage: telr [-h] -i READS -r REFERENCE -l LIBRARY [--aligner ALIGNER]
[--assembler ASSEMBLER] [--polisher POLISHER] [-x PRESETS]
[-p POLISH_ITERATIONS] [-o OUT] [-t THREAD] [-g GAP]
[-v OVERLAP] [--flank_len FLANK_LEN]
[--af_flank_interval AF_FLANK_INTERVAL]
[--af_flank_offset AF_FLANK_OFFSET]
[--af_te_interval AF_TE_INTERVAL] [--af_te_offset AF_TE_OFFSET]
[--different_contig_name] [--minimap2_family] [-k]
Program for detecting non-reference TEs in long read data
required arguments:
-i READS, --reads READS
reads in fasta/fastq format or read alignments in bam
format
-r REFERENCE, --reference REFERENCE
reference genome in fasta format
-l LIBRARY, --library LIBRARY
TE consensus sequences in fasta format
optional arguments:
-h, --help show this help message and exit
--aligner ALIGNER choose method for read alignment, please provide
'nglmr' or 'minimap2' (default = 'nglmr')
--assembler ASSEMBLER
Choose the method to be used for local contig assembly
step, please provide 'wtdbg2' or 'flye' (default =
'wtdbg2')
--polisher POLISHER Choose the method to be used for local contig
polishing step, please provide 'wtdbg2' or 'flye'
(default = 'wtdbg2')
-x PRESETS, --presets PRESETS
parameter presets for different sequencing
technologies, please provide 'pacbio' or 'ont'
(default = 'pacbio')
-p POLISH_ITERATIONS, --polish_iterations POLISH_ITERATIONS
iterations of contig polishing (default = 1)
-o OUT, --out OUT directory to output data (default = '.')
-t THREAD, --thread THREAD
max cpu threads to use (default = '1')
-g GAP, --gap GAP max gap size for flanking sequence alignment (default
= '20')
-v OVERLAP, --overlap OVERLAP
max overlap size for flanking sequence alignment
(default = '20')
--flank_len FLANK_LEN
flanking sequence length (default = '500')
--af_flank_interval AF_FLANK_INTERVAL
5' and 3'flanking sequence interval size used for
allele frequency estimation (default = '100')
--af_flank_offset AF_FLANK_OFFSET
5' and 3' flanking sequence offset size used for
allele frequency estimation (default = '200')
--af_te_interval AF_TE_INTERVAL
5' and 3' te sequence interval size used for allele
frequency estimation (default: '50')
--af_te_offset AF_TE_OFFSET
5' and 3' te sequence offset size used for allele
frequency estimation (default: '50')
--different_contig_name
If provided then TELR does not require the contig name
to match before and after annotation liftover
(default: require contig name to be the same before
and after liftover)
--minimap2_family If provided then minimap2 will be used to annotate TE
families in the assembled contigs (default: use
repeatmasker for contig TE annotation)
-k, --keep_files If provided then all intermediate files will be kept
(default: remove intermediate files)
TELR requires long reads in FASTA/FASTQ format or read alignments in BAM format from BWA-MEM (use -M and -x parameter), Minimap2 (with Cigar & MD string) or NGMLR, a reference genome assembly in FASTA format (which must be the same as the one used to align the reads, if read alignments are provided), and TE consensus sequence in FASTA format. Here is a template with the names of the required and optional parameters.
telr -i (--reads) <reads in fasta/fastq format or read alignments in bam format> \
-r (--reference) <reference genome in fasta format> \
-l (--library) <TE consensus sequences in fasta format>
In addition to the required program options listed above, there are some optional arguments. The full list of program options with descriptions can also be obtained by running telr -h.
-x/--presets <str>Preset for different sequencing technologies, please provide 'pacbio' or 'ont' (default = 'pacbio').--aligner <str>Method for read alignment, please provide 'nglmr' or or 'minimap2' (default = 'nglmr').--assembler <str>Method for for local contig assembly step, please provide 'wtdbg2' or or 'flye' (default = 'wtdbg2').--polisher <str>Method for for local contig polishing step, please provide 'wtdbg2' or or 'flye' (default = 'wtdbg2').-p/--polish_iterations <int>Iterations of contig polishing (default = '1').-o/--out <str>Output directory (default = '.').-t/--thread <int>Maximum cpu threads to use (default = '1').-g/--gap <int>Maximum gap size between sequence alignments of two contig flanks (default= '50').-v/--overlap <int>Maximum overlap size between sequence alignments of two contig flanks (default= '50').--flank_len <int>flanking sequence length in the TELR assembled contigs (default= '500').--af_flank_interval <int>5' and 3' flanking sequence interval size used for allele frequency estimation (default= '100').--af_flank_offset <int>5' and 3' flanking sequence offset size used for allele frequency estimation (default= '200').--af_te_interval <int>5' and 3' TE interval size used for allele frequency estimation (default: '50').--af_te_offset <int>5' and 3' TE offset size used for allele frequency estimation (default= '50').--different_contig_nameIf provided then TELR does not require the contig name to match before and after annotation liftover (default: require contig name to be the same before and after liftover).--minimap2_familyIf provided then minimap2 will be used to annotate TE families in the assembled contigs (default: use repeatmasker for contig TE annotation).-k/--keep_filesIf provided then all intermediate files will be kept (default: remove intermediate files).