https://github.com/philres/ngmlr
NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations
https://github.com/philres/ngmlr
alignment bioconda docker long-read mapper next-generation-sequencing oxford-nanopore pacbio structural-variations
Last synced: 6 months ago
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NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations
- Host: GitHub
- URL: https://github.com/philres/ngmlr
- Owner: philres
- License: mit
- Created: 2016-09-01T13:11:53.000Z (about 9 years ago)
- Default Branch: master
- Last Pushed: 2021-08-16T04:02:11.000Z (about 4 years ago)
- Last Synced: 2023-10-25T18:33:57.415Z (almost 2 years ago)
- Topics: alignment, bioconda, docker, long-read, mapper, next-generation-sequencing, oxford-nanopore, pacbio, structural-variations
- Language: C++
- Homepage:
- Size: 35.4 MB
- Stars: 277
- Watchers: 22
- Forks: 40
- Open Issues: 48
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
### Quick start
Download [binary](https://github.com/philres/ngmlr/releases/tag/v0.2.6) from github and unzip or [](http://bioconda.github.io/recipes/ngmlr/README.html) or pull docker [](https://hub.docker.com/r/philres/ngmlr/). For updates follow [](https://twitter.com/philres1)
Download precompiled version:
```bash
wget https://github.com/philres/ngmlr/releases/download/v0.2.7/ngmlr-0.2.7-linux-x86_64.tar.gz
tar xvzf ngmlr-0.2.7-linux-x86_64.tar.gz
cd ngmlr-0.2.7/
```
For PacBio data run:
```bash
ngmlr -t 4 -r reference.fasta -q reads.fastq -o test.sam
```
For Oxford Nanopore run:
```bash
ngmlr -t 4 -r reference.fasta -q reads.fastq -o test.sam -x ont
```
### Introduction
CoNvex Gap-cost alignMents for Long Reads (ngmlr) is a long-read mapper designed to sensitively align PacBio or Oxford Nanopore to (large) reference genomes. It was designed to quickly and correctly align the reads, including those spanning (complex) structural variations. Ngmlr uses an SV aware k-mer search to find approximate mapping locations for a read and then a banded Smith-Waterman alignment algorithm to compute the final alignment. Ngmlr uses a convex gap cost model that penalizes gap extensions for longer gaps less than for shorter ones to compute precise alignments. The gap model allows ngmlr to account for both the sequencing error and real genomic variations at the same time and makes it especially effective at more precisely identifying the position of breakpoints stemming from structural variations. The k-mer search helps to detect and split reads that cannot be aligned linearly, enabling ngmlr to reliably align reads to a wide range of different structural variations including nested SVs (e.g. inversions flanked by deletions).
With 10 cores (AMD Opteron 6348), ngmlr currently takes about 90 minutes and 10 GB RAM for aligning 3Gbp (~ 1x human data) of PacBio reads.
### Citation:
Please see and cite our paper:
https://www.nature.com/articles/s41592-018-0001-7
**Poster & Talks:**
[Accurate and fast detection of complex and nested structural variations using long read technologies](http://schatzlab.cshl.edu/presentations/2016/2016.10.28.BIODATA.PacBioSV.pdf)
Biological Data Science, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 26 - 29.10.2016
[NGMLR: Highly accurate read mapping of third generation sequencing reads for improved structural variation analysis](http://www.cibiv.at/~philipp_/files/gi2016_poster_phr.pdf)
Genome Informatics 2016, Wellcome Genome Campus Conference Centre, Hinxton, Cambridge, UK, 19.09.-2.09.2016
### Parameters
```
Usage: ngmlr [options] -r -q [-o ]
Input/Output:
-r , --reference
(required) Path to the reference genome (FASTA/Q, can be gzipped)
-q , --query
Path to the read file (FASTA/Q) [/dev/stdin]
-o , --output
Path to output file [stdout]
--skip-write
Don't write reference index to disk [false]
--bam-fix
Report reads with > 64k CIGAR operations as unmapped. Required to be compatible with the BAM format [false]
--rg-id
Adds RG:Z: to all alignments in SAM/BAM [none]
--rg-sm
RG header: Sample [none]
--rg-lb
RG header: Library [none]
--rg-pl
RG header: Platform [none]
--rg-ds
RG header: Description [none]
--rg-dt
RG header: Date (format: YYYY-MM-DD) [none]
--rg-pu
RG header: Platform unit [none]
--rg-pi
RG header: Median insert size [none]
--rg-pg
RG header: Programs [none]
--rg-cn
RG header: sequencing center [none]
--rg-fo
RG header: Flow order [none]
--rg-ks
RG header: Key sequence [none]
General:
-t , --threads
Number of threads [1]
-x , --presets
Parameter presets for different sequencing technologies [pacbio]
-i <0-1>, --min-identity <0-1>
Alignments with an identity lower than this threshold will be discarded [0.65]
-R , --min-residues
Alignments containing less than or ( * read length) residues will be discarded [0.25]
--no-smallinv
Don't detect small inversions [false]
--no-lowqualitysplit
Split alignments with poor quality [false]
--verbose
Debug output [false]
--no-progress
Don't print progress info while mapping [false]
Advanced:
--match
Match score [2]
--mismatch
Mismatch score [-5]
--gap-open
Gap open score [-5]
--gap-extend-max
Gap open extend max [-5]
--gap-extend-min
Gap open extend min [-1]
--gap-decay
Gap extend decay [0.15]
-k <10-15>, --kmer-length <10-15>
K-mer length in bases [13]
--kmer-skip
Number of k-mers to skip when building the lookup table from the reference [2]
--bin-size
Sets the size of the grid used during candidate search [4]
--max-segments
Max number of segments allowed for a read per kb [1]
--subread-length
Length of fragments reads are split into [256]
--subread-corridor
Length of corridor sub-reads are aligned with [40]
```
### Running with docker
```bash
docker run -ti -v /home/user/data/:/home/user/data/ philres/ngmlr ngmlr -r /home/user/data/ref.fa -q /home/user/data/reads.fasta -o /home/user/data/output.sam
```
### Building ngmlr from source
OS: Linux and Mac OSX:
Requirements: zlib-dev, cmake, gcc/g++ (>=4.8.2)
```bash
git clone https://github.com/philres/ngmlr.git
cd ngmlr/
mkdir -p build
cd build/
cmake ..
make
cd ../bin/ngmlr-*/
./ngmlr
```
### Building ngmlr for linux with docker
```bash
git clone https://github.com/philres/ngmlr.git
mkdir -p ngmlr/build
docker run -v `pwd`/ngmlr:/ngmlr philres/nextgenmaplr-buildenv bash -c "cd /ngmlr/build && cmake .. && make"
`pwd`/ngmlr/bin/ngmlr-*/ngmlr
```
### NGMLR progress information
Example:
```
Processed: 92198 (0.66), R/S: 37.44, RL: 8857, Time: 2.00 5.00 11.62, Align: 0.96, 490, 0.81
```
92198 reads were processed so far
66 % of the 92198 reads were mapped (with > 25 % of their bp mapped)
37.44 are mapped on average per second
8857 is the average read length so far
"Time" and "Align" are for debugging purpose and will be removed.
### Datasets used in the mansucript:
We provide the NGMLR aligned reads and the Sniffles calls for the data sets used:
Arabidopsis trio: [http://labshare.cshl.edu/shares/schatzlab/www-data/fsedlaze/Sniffles/Arabidopsis_trio](http://labshare.cshl.edu/shares/schatzlab/www-data/fsedlaze/Sniffles/Arabidopsis_trio) .
Genome in a Bottle trio:
+ Mappings: [ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG002_NA24385_son/PacBio_MtSinai_NIST/Baylor_NGMLR_bam_GRCh37/](ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG002_NA24385_son/PacBio_MtSinai_NIST/Baylor_NGMLR_bam_GRCh37/) .
+ SV calls: [http://labshare.cshl.edu/shares/schatzlab/www-data/fsedlaze/Sniffles/GiaB/](http://labshare.cshl.edu/shares/schatzlab/www-data/fsedlaze/Sniffles/GiaB/)
NA12878: [http://labshare.cshl.edu/shares/schatzlab/www-data/fsedlaze/Sniffles/NA12878/](http://labshare.cshl.edu/shares/schatzlab/www-data/fsedlaze/Sniffles/NA12878/) .
SKBR3: [http://labshare.cshl.edu/shares/schatzlab/www-data/fsedlaze/Sniffles/Skbr3/](http://labshare.cshl.edu/shares/schatzlab/www-data/fsedlaze/Sniffles/Skbr3/) .