Lr_gapcloser

Introduction

LR_Gapcloser is a gap closing tool using long reads from studied species.

For more information, please check:
BioContainers: https://biocontainers.pro/tools/lr_gapcloser
Home page: https://github.com/CAFS-bioinformatics/LR_Gapcloser

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster

Version(s)

ANVIL

20180904

NEGISHI

20180904

Commands

  • LR_Gapcloser.sh

  • best-match-LR.pl

  • block_align.pl

  • bwa

  • change_case_fasta.pl

  • complete_retriver.pl

  • complete_substitute_limiter.pl

  • complete_ultimate_elect.pl

  • coverage_calculator.pl

  • coverage_filter.pl

  • find_sequnce_file.pl

  • form_sequence.pl

  • format_fa.pl

  • further_partial_select.pl

  • gap_bridging.pl

  • gap_finder.pl

  • group_partial.pl

  • info_formatter.pl

  • info_pacify.pl

  • join_LRlength.pl

  • last_Drepeat.pl

  • partial_ultimate_elect.pl

  • remove_wrong3.pl

  • retrieve-unique-alignment.pl

  • retriever_backfill.pl

  • same_filter.pl

  • split

  • tag_alignment_filter.pl

  • tag_distance_filter_classify.pl

  • tag_generator.pl

  • tag_orientation_corrector.pl

Module

You can load the modules by:

module load biocontainers
module load lr_gapcloser

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run lr_gapcloser on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -p wholenode        # Partition name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=lr_gapcloser
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers lr_gapcloser

# Your lr_gapcloser workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=lr_gapcloser
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers lr_gapcloser

# Your lr_gapcloser workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=lr_gapcloser
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers lr_gapcloser

# Your lr_gapcloser workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=lr_gapcloser
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers lr_gapcloser

# Your lr_gapcloser workflow...

#!/bin/bash
#SBATCH -A queue     # Queue name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=lr_gapcloser
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers lr_gapcloser

# Your lr_gapcloser workflow...