- v0.2.1: Greatly reduces processing time for both WGS and telobait modes
- v0.1.0: Supports input of whole-genome sequencing (WGS) long-read data
Telomap is a tool to identify and analyse telomeric reads within WGS or telobait-captured long-read sequencing data.
Two modes of running
- Telobait mode: requires data generated from a wet lab telomere capturing method described in our publication.
- WGS mode: requires vanilla long-read data generated from whole-genome sequencing runs.
General workflow
- De-multiplex barcoded samples (for telobait-capture data)
- Identify long-reads that contain telomeric sequences
- Cluster subtelomeric region of telomeric reads to generate unique consensus anchor sequences
- Map subtelomeric anchor sequences to chromosome ends based on T2T-CHM13 assembly
- Analyze the distribution of non-canonical telomeric motifs (Telomere variant sequences (TVS))
- Generate QC and analytic plots
git clone https://github.com/cytham/telomap.git
cd telomap
pip install .telomap [options] [RUN_MODE] [READS] [WORK_DIRECTORY]
# For WGS mode with 24 threads
telomap wgs /path/to/reads.fastq.gz /path/to/work_dir -t 24
# For telobait mode with 24 threads
telomap telobait /path/to/reads.fastq.gz /path/to/work_dir -t 24 -c /path/to/capture_oligo.fa -b /path/to/barcodes.fa
# See below for instructions to create capture_oligo.fa and barcodes.fa filesusage: telomap [options] [RUN_MODE] [READS] [WORK_DIRECTORY]
Telomap is a tool for analyzing telomeric reads from WGS or telobait-capture long-read sequencing data
required arguments:
[RUN_MODE] run modes:
wgs (whole genome sequencing mode)
telobait (telobait capture mode)
[READS] path to input reads (fasta/fastq/bam/pacbio-bam)
[WORK_DIRECTORY] path to work directory
optional arguments:
-c path, --capoligo path
path to capture oligo fasta file
-b path, --barcodes path
path to barcodes fasta file
-n str, --name str name prefix for output files [sample]
-m str, --motif str telomeric motif sequence [TTAGGG]
--oligoscore float minimum alignment score fraction required
for capture oligo sequence match [1]
--barscore float minimum alignment score fraction required
for barcode sequence match. Warning: Reducing
this value may lead to multiple barcode mapping
per read, causing high read omission. [1]
-t int, --threads int
specify number of threads [1]
-v, --version print version
-q, --quiet hide verbose
-h, --help show this help message and exit
The capture oligo sequence refers to the sequence after the barcode on the telobait, while the barcode sequence refers to the start of the telobait until the end of the barcode.
See example below:
# Telobait
5'-ATCGANNNNNNNNGATGCCAGATGCACGGAGCA...-Biotin-3'
|||||||||||||||||||||||||||||||||
3'-CCAATCTAGCTNNNNNNNNCTACGGTCTACGTGCCTCGT...-5'
where NNNNNNNN is the sample barcode
# The capture_oligo.fa should contain the following sequence
>capture_oligo
GATGCCAGATGCACGGAGCA
# The barcodes.fa should contain the following sequences
>sample1
ATCGACGGTTCAA
>sample2
ATCGAGCTGGATT
>sample3
ATCGATAACTCGG
| Output | Comment |
|---|---|
| sample.telomap.tsv | Main output table containing per read information |
| sample.telomap.anchors.tsv | Table containing details of subtelomeric anchor sequences for chromosome-end mapping |
| plots | Directory containing analytic plots |
| plots_QC | Directory containing QC plots |
| # | Column name | Comment |
|---|---|---|
| 1 | RNAME | Read ID |
| 2 | OLIGO | Name of capture oligo detected (will be NA for WGS mode) |
| 3 | BARCODE | Detected sample barcode (will be NA for WGS mode) |
| 4 | STRAND | Strand of read with reference to motif |
| 5 | MOTIF | Telomeric motif detected |
| 6 | RLEN | Read length |
| 7 | RAW_TELOMERE_LEN | Length of telomeric region in bases demarcated by TELOMERE_START and TELOMERE_END (See below) |
| 8 | TELOMERE_LEN | Length of telomeric region in bases after excluding all non-telomeric sequences within RAW_TELOMERE_LEN (See below) |
| 9 | TELOMERE_END_MOTIF | Last six 3' telomeric bases within telomeric region on read |
| 10 | TRF_COUNT | Number of TRF binding motifs detected (5'-TTAGGGTTA-3') |
| 11 | CHROM | Detected chromosomal end or unmappable sub-telomeric cluster (i.e. begins with "U") |
| 12 | TELOMERE_START | Refers to the 1-based position on a read at the 5′ end of the telomeric region as defined by containing at least two consecutive telomeric repeats (5′-TTAGGGTTAGGG-3′) |
| 13 | TELOMERE_END | Refers to the 1-based position on a read at the 3' end of the telomeric region as defined by being adjacent to the telobait sequence in telobait mode, or the 3' most complete/partial telomeric sequence in WGS mode |
| 14 | NUM_PASS | Number of full-length subreads (only for pacbio BAM data) |
| 15 | RQUAL | Read quality (only for pacbio BAM data) |
Example read: 5'-ATAGGCATGC TTAGGGTTAGGG TTAGGG TTAGGG TTAGGG TG TTAGGG G TTAGGG TTGGG TTAGGG TTAGGGTTAG ATACAG-3'
| Term | Value | Sequence | Comment |
|---|---|---|---|
| TELOMERE_START | 11 | TTAGGGTTAGGG | Positions 11-22 |
| TELOMERE_END | 76 | TTAGGGTTAG | Positions 67-76 |
| RAW_TELOMERE_LEN | 66 | TTAGGGTTAGGG TTAGGG TTAGGG TTAGGG TG TTAGGG G TTAGGG TTGGG TTAGGG TTAGGGTTAG | TELOMERE_START(76)-TELOMERE_END(11)+1=66 |
| TELOMERE_LEN | 54 | TTAGGGTTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG | Motif count(9)*motif length(6)=54 |
| TELOMERE_END_MOTIF | GGTTAG | GGTTAG | - |
| # | Column name | Comment |
|---|---|---|
| 1 | BARCODE | Detected sample barcode (will be NA for WGS mode) |
| 2 | ANCHOR_READ | Read ID of representative read for the anchor cluster |
| 3 | ANCHOR_SEQ | Consensus subtelomeric anchor sequence |
| 4 | READ_SUPPORT | Number of reads supporting subtelomeric anchor sequence |
| 5 | CHROM | Chromosomal end mapped by anchor sequence or unmappable anchor ID (i.e. begins with "U") |
- Linux (x86_64 architecture, tested in Ubuntu 22.04.1)
See CHANGELOG
Tham CY, Poon L, Yan T, Koh JYP, Ramlee MK, Teoh VSI, Zhang S, Cai Y, Hong Z, Lee GS, Liu J, Song HW, Hwang WYK, Teh BT, Tan P, Xu L, Koh AS, Osato M, Li S. High-throughput telomere length measurement at nucleotide resolution using the PacBio high fidelity sequencing platform. Nat Commun. 2023 Jan 17;14(1):281. doi: 10.1038/s41467-023-35823-7. PMID: 36650155; PMCID: PMC9845338. https://www.nature.com/articles/s41467-023-35823-7
- Tham Cheng Yong - cytham
This project is licensed under GNU General Public License - see LICENSE.txt for details.
- Current chromosomal end mapping is incomplete