GraphMap - A highly sensitive and accurate mapper for long, error-prone reads

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GraphMap is a highly sensitive and accurate mapper for long, error-prone reads. It offers a number of valuable features, such as mapping position agnostic to alignment parameters, high sensitivity and precision, handling circular genomes, meaningful mapping quality, various alignment strategies, and more.

References:

Ivan Sović, Mile Šikić, Andreas Wilm, Shannon Nicole Fenlon, Swaine Chen & Niranjan Nagarajan
Fast and sensitive mapping of nanopore sequencing reads with GraphMap,
Nature Communications volume 7, Article number: 11307 (2016) .

Documentation

GraphMap GitHub page

Important Notes

Module Name: graphmap (see the modules page for more information)
Implemented as a Singularity container
Unusual environment variables set
- GM_HOME installation directory
- GM_HOME executable directory

Interactive job

Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --mem=4g
[user@cn3316 ~]$ module load graphmap 
[+] Loading graphmap 0.5.2  ...
[user@cn3316 ~]$ graphmap -h
...

Usage:
  graphmap tool

Options
    tool       STR   Specifies the tool to run:
                       align - the entire GraphMap pipeline.
                       owler - Overlapping With Long Erroneous Reads.

The grapgmap application can be used as follows:

**Align** all reads from a given FASTA/FASTQ file using anchored alignment approach:

[user@cn3316 ~]$  graphmap align -r escherichia_coli.fa -d reads.fastq -o alignments.sam

**Overlap** all reads from a given FASTA/FASTQ file and report overlaps in MHAP format (fast):

[user@cn3316 ~]$ graphmap owler -r reads.fa -d reads.fa -o overlaps.mhap

**Align** all reads to a transcriptome sequence:

[user@cn3316 ~]$ graphmap align -r scerevisiae.fa --gtf scerevisiae.gtf -d reads.fastq -o alignments.sam

Align all reads and report alignments using the extended CIGAR format.

[user@cn3316 ~]$ graphmap align -r escherichia_coli.fa -d reads.fastq -o alignments.sam --extcigar

Align all reads from a given FASTA/FASTQ file with default number of threads using semiglobal bit-vector alignment:

[user@cn3316 ~]$ graphmap align -a sg -r escherichia_coli.fa -d reads.fastq -o alignments.sam

Overlap all reads from a given FASTA/FASTQ in a full GraphMap mode with generating alignments (slow):

[user@cn3316 ~]$ graphmap align -x overlap -r reads.fa -d reads.fa -o overlaps.sam

Align reads using the Gotoh for semiglobal alignment:

[user@cn3316 ~]$ graphmap align -a sggotoh -r escherichia_coli.fa -d reads.fastq -o alignments.sam

Align reads using Gotoh alignment with anchored approach:

[user@cn3316 ~]$ graphmap align -a anchorgotoh -r escherichia_coli.fa -d reads.fastq -o alignments.sam

Process reads from a circular genome:

[user@cn3316 ~]$ graphmap align -C -r escherichia_coli.fa -d reads.fastq -o alignments.sam

Threshold the E-value of alignments to 1e-100. Alignments with E-value > 1e-100 will be called unmapped:

[user@cn3316 ~]$ graphmap align --evalue 1e-100 -r escherichia_coli.fa -d reads.fastq -o alignments.sam

Output all secondary alignments instead of only one best:

[user@cn3316 ~]$ graphmap align --secondary -r escherichia_coli.fa -d reads.fastq -o alignments.sam

Control the similarity for secondary alignments. All alignments to within F*num_covered_bases from the best will be output.

[user@cn3316 ~]$ graphmap align --secondary -F 0.05 -r escherichia_coli.fa -d reads.fastq -o alignments.sam

Limit the number of threads to 8, and load reads in batches of 50MB:

[user@cn3316 ~]$ graphmap align -t 8 -B 50 -r escherichia_coli.fa -d reads.fastq -o alignments.sam

Align reads using more sensitive parameters for Illumina data:

[user@cn3316 ~]$ graphmap align -x illumina -r escherichia_coli.fa -d reads.fastq -o alignments.sam

Load all reads in one batch and align only the first 1000 reads:

[user@cn3316 ~]$ graphmap align -B 0 -n 1000 -r escherichia_coli.fa -d reads.fastq -o alignments.sam

Rebuild the index if it already exists:

[user@cn3316 ~]$ graphmap align --rebuild-index -r escherichia_coli.fa -d reads.fastq -o alignments.sam

Generate only the index.

[user@cn3316 ~]$ graphmap align -I -r escherichia_coli.fa

Run a debug version of GraphMap (build with "make debug") and verbose the SAM output to see various info about alignment:

[user@cn3316 ~]$ graphmap-debug align -b 3 -r escherichia_coli.fa -d reads.fastq -o alignments.sam

End the interactive session:

[user@cn3316 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$