CLI reference¶
Generated from --help. Run the commands yourself for the authoritative text.
teloclip¶
Usage: teloclip [OPTIONS] [COMMAND] [ARGS]...
A tool for the recovery of unassembled telomeres from soft-clipped read
alignments.
Options:
--version Show the version and exit.
--help Show this message and exit.
Commands:
extend Extend contigs using overhang analysis from soft-clipped...
extract Extract overhanging reads for each end of each reference contig.
filter Filter SAM file for clipped alignments containing unassembled...
teloclip filter¶
Reads SAM on stdin, writes SAM on stdout.
Usage: teloclip filter [OPTIONS] [SAMFILE]
Filter SAM file for clipped alignments containing unassembled telomeric
repeats.
Options:
--ref-idx PATH Path to fai index for reference fasta. Index
fasta using `samtools faidx FASTA`
[required]
--min-clip INTEGER Require clip to extend past ref contig end
by at least N bases. Default: 1
--max-break INTEGER Tolerate max N unaligned bases before contig
end. Default: 50
--motifs TEXT If set keep only reads containing given
motif/s from comma delimited list of
strings. By default also search for reverse
complement of motifs. i.e. TTAGGG,TTAAGGG
will also match CCCTAA,CCCTTAA
--no-rev If set do NOT search for reverse complement
of specified motifs.
--keep-secondary If set, include secondary alignments in
output. Default: Off (exclude secondary
alignments).
--fuzzy If set, tolerate +/- 1 variation in motif
homopolymer runs i.e. TTAGGG ->
T{1,3}AG{2,4}. Default: Off
-r, --min-repeats INTEGER Minimum number of sequential pattern matches
required for a hit to be reported. Default:
1
--min-anchor INTEGER Minimum number of aligned bases (anchor)
required on the non-clipped portion of the
read. Default: 100
--match-anywhere If set, motif match may occur in unclipped
region of reads.
--log-level [debug|info|warning|error]
Logging level (default: INFO).
--logfile PATH Also write log messages to this file (parent
directories are created).
--help Show this message and exit.
teloclip extract¶
Reads SAM on stdin, writes per-contig-end FASTA files.
Usage: teloclip extract [OPTIONS] [SAMFILE]
Extract overhanging reads for each end of each reference contig. Reads are
always written to output files.
Options:
--ref-idx PATH Path to fai index for reference fasta. Index
fasta using `samtools faidx FASTA`
[required]
--prefix TEXT Use this prefix for output files. Default:
None.
--extract-dir PATH Write extracted reads to this directory.
Default: cwd.
--min-clip INTEGER Require clip to extend past ref contig end
by at least N bases. Default: 1
--max-break INTEGER Tolerate max N unaligned bases before contig
end. Default: 50
--min-anchor INTEGER Minimum anchored alignment length required
(default: 100).
--min-mapq INTEGER Minimum mapping quality required (default:
0).
--keep-secondary If set, include secondary alignments in
output. Default: Off (exclude secondary
alignments).
--include-stats Include mapping quality, clip length, and
motif counts in FASTA headers.
--count-motifs TEXT Comma-delimited motif sequences to count in
overhang regions (e.g., "TTAGGG,CCCTAA").
--fuzzy-count Use fuzzy motif matching allowing ±1
character variation when counting motifs.
--buffer-size INTEGER Number of sequences to buffer before writing
(default: 1000).
--output-format [fasta|fastq] Output format for extracted sequences
(default: fasta).
--report-stats Write extraction statistics to file in
output directory.
--no-mask-overhangs Do not convert overhang sequences to
lowercase.
--log-level [DEBUG|INFO|WARNING|ERROR]
Logging level (default: INFO).
--logfile PATH Also write log messages to this file (parent
directories are created).
--help Show this message and exit.
teloclip extend¶
Reads an indexed BAM and FASTA from disk; cannot read a stream.
Usage: teloclip extend [OPTIONS] BAM_FILE REFERENCE_FASTA
Extend contigs using overhang analysis from soft-clipped alignments.
Options:
--output-fasta PATH Extended FASTA output file
--stats-report PATH Statistics report output file
--exclude-outliers DEPRECATED and ignored. Contigs with
anomalous overhang coverage are now reported
for review rather than silently dropped;
exclude them with --exclude-contigs if you
agree with the assessment.
--outlier-threshold FLOAT Modified z-score above which a contig end is
reported as having anomalous overhang
coverage (default: 3.5)
--min-overhangs INTEGER Minimum supporting overhangs required
(default: 1)
--max-homopolymer INTEGER Maximum homopolymer run length allowed
(default: 500)
--min-extension INTEGER Minimum novel bases an overhang must
contribute to be used (default: 1)
--min-clip INTEGER Require clip to extend past the contig end
by at least N bases (default: 1)
--max-break INTEGER Maximum gap allowed between alignment and
contig end (default: 50)
--min-anchor INTEGER Minimum anchor length required for alignment
(default: 100)
--dry-run Report extensions without modifying
sequences
--count-motifs TEXT Comma-delimited motif sequences to count in
overhang regions (e.g., "TTAGGG,CCCTAA")
--fuzzy-count Use fuzzy motif matching allowing ±1
character variation when counting motifs
--prefix TEXT Prefix for default output filenames
(default: teloclip_extended)
--screen-terminal-bases INTEGER
Number of terminal bases to screen for
motifs in original contigs (default: 0,
disabled)
--exclude-contigs TEXT Comma-delimited list of contig names to
exclude from extension (e.g.,
"chrM,chrC,scaffold_123")
--exclude-contigs-file PATH Text file containing contig names to exclude
(one per line)
--log-level [debug|info|warning|error]
Logging level (default: INFO).
--logfile PATH Also write log messages to this file (parent
directories are created).
--html-report PATH Write a self-contained HTML report showing
every overhang read aligned against the
contig terminus it supports, plus overhang
depth across the assembly.
--html-max-reads INTEGER Maximum overhang reads rendered per contig
end in the HTML report (default: 25). Reads
contributing the most sequence are shown
first.
--overhang-log PATH Write a TSV describing every accepted
overhang read: contig, end, gap from the
contig terminus, clip length and overhang
length.
--help Show this message and exit.