Address of the bookmark: http://pacb.com/blog/the-hifi-difference-true-long-reads-vs-synthetic-long-reads/

• BigDataScript – A cross-system scripting language for working with big data pipelines in computer systems of different sizes and capabilities. [ paper-2014 | web ]
• Bpipe – A small language for defining pipeline stages and linking them together to make pipelines. [ web ]
• Common Workflow Language – a specification for describing analysis workflows and tools that are portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing (HPC) environments. [ web ]
• Cromwell – A Workflow Management System geared towards scientific workflows. [ web ]
• Galaxy – a popular open-source, web-based platform for data intensive biomedical research. Has several features, from data analysis to workflow management to visualization tools. [ paper-2018 | web ]
• Nextflow (recommended) – A fluent DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner. [ paper-2018 | web ]
• Ruffus – Computation Pipeline library for python widely used in science and bioinformatics. [ paper-2010 | web ]
• SeqWare – Hadoop Oozie-based workflow system focused on genomics data analysis in cloud environments. [ paper-2010 | web ]
• Snakemake – A workflow management system in Python that aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment. [ paper-2018 | web ]
• Workflow Descriptor Language – Workflow standard developed by the Broad. [ web ]

The prepint version is found on http://www.biorxiv.org/content/early/2017/08/09/173872

It uses the pyPaSWAS framework for sequence alignment (https://github.com/swarris/pyPaSWAS)

Address of the bookmark: https://github.com/swarris/Pacasus

• Binaries for Linux/macOS
• From sources for Linux/macOS
• From sources for Windows

Address of the bookmark: https://github.com/imgag/ngs-bits

For knowledge about Linux and their importance amongst bioinformatician plesae read this article "An introduction to Linux for bioinformatics" by Paul Stothard.

Linux cheat sheet at http://bioinformaticsonline.com/file/view/87/linux-cheat-sheet

Please browse for futher useful linux pages on right hand side ...

The following table shows SLURM commands on the SOE cluster.

For more information, run man on the commands above. See some examples below.

1. Info about the partitions and nodes
List all the partitions available to you and the nodes therein:

sinfo

Nodes in state idle can accept new jobs.

Show a partition configuratuin, for example, SOE_main

scontrol show partition=SOE_main

Show current info about a specific node:

scontrol show node=<nodename>

You can also specify a group of nodes in the command above. For example, if your MPI job is running across soenode05,06,35,36, you can execute the command below to get the info on the nodes you are interested in:

scontrol show node=soenode[05-06,35-36]

An informative parameter in the output to look at would be CPULoad. It allows you to see how your application utilizes the CPUs on the running nodes.

2. Submit scripts
The header in a submit script specifies job name, partition (queue), time limit, memory allocation, number of nodes, number of cores, and files to collect standard output and error at run time, for example

#!/bin/bash

#SBATCH --job-name=OMP_run     # job name, "OMP_run"
#SBATCH --partition=SOE_main   # partition (queue)
#SBATCH -t 0-2:00              # time limit: (D-HH:MM) 
#SBATCH --mem=32000            # memory per node in MB 
#SBATCH --nodes=1              # number of nodes
#SBATCH --ntasks-per-node=16   # number of cores
#SBATCH --output=slurm.out     # file to collect standard output
#SBATCH --error=slurm.err      # file to collect standard errors

If the time limit is not specified in the submit script, SLURM will assign the default run time, 3 days. This means the job will be terminated by SLURM in 72 hrs. The maximum allowed run time is two weeks, 14-0:00.
If the memory limit is not requested, SLURM will assign the default 16 GB. The maximum allowed memory per node is 128 GB. To see how much RAM per node your job is using, you can run commands sacct or sstat to query MaxRSS for the job on the node - see examples below.
Depending on a type of application you need to run, the submit script may contain commands to create a temporary space on a computational node - see the discussion about using the file systems on the cluster.
Then it sets the environment specific to the application and starts the application on one or multiple nodes - see sbatch sample scripts in directory /usr/local/Samples on soemaster1.hpc.rutgers.edu.
You can submit your job to the cluster with sbatch command:

sbatch myscript.sh

3. Query job information
List all currently submitted jobs in running and pending states for a user:

squeue -u <username>

Command squeue can be run with format options to expose specific information, for example, when pending job #706 is scheduled to start running:

squeue -j 706 --format="%S"

START_TIME
2015-04-30T09:54:32

More info can be shown by placing additional format options, for example:

squeue -j 706 --format="%i %P %j %u %T %l %C %S"

JOBID PARTITION   NAME    USER STATE   TIMELIMIT  CPUS START_TIME
706   SOE_main  Par_job_3 mike PENDING 3-00:00:00 64   2015-04-30T09:54:32

To see when all the jobs, pending in the queue, are scheduled to start:

squeue --start 

List all running and completed jobs for a user

sqlog -u <username>

or

sqlog -j <JobID>

The following appreviations are used for the job states:

       CA   CANCELLED      Job was cancelled.

       CD   COMPLETED      Job completed normally.

       CG   COMPLETING     Job is in the process of completing.

       F    FAILED         Job termined abnormally.

       NF   NODE_FAIL      Job terminated due to node failure.

       PD   PENDING        Job is pending allocation.

       R    RUNNING        Job currently has an allocation.

       S    SUSPENDED      Job is suspended.

       TO   TIMEOUT        Job terminated upon reaching its time limit.

You can specify the fields you would like to see in the output of sqlog:

sqlog --format=list

The command below, for example, provides Job ID, user name, exit state, start date-time, and end date-time for job #2831:

sqlog -j 2831 --format=jid,user,state,start,end

List status info for a currently running job:

sstat -j <jobid>

A formatted output can be used to gain only a specific info, for example, the maximum resident RAM usage on a node:

sstat --format="JobID,MaxRSS" -j <jobid>

To get statistics on completed jobs by jobID:

sacct --format="JobID,JobName,MaxRSS,Elapsed" -j <jobid>

To view the same information for all jobs of a user:

sacct --format="JobID,JobName,MaxRSS,Elapsed" -u <username>

To print a list of fields that can be specified with the --format option:

sacct --helpformat

For example, to get Job ID, Job name, Exit state, start date-time, and end date-time for job #2831:

sacct -j 2831 --format="JobID,JobName,State,Start,End"

Another useful command to gain information about a running job is scontrol:

scontrol show job=<jobid>

4. Cancel a job
To cancel one job:

scancel <jobid>

To cancel one job and delete the TMP directory created by the submit script on a node:

sdel <jobid>

To cancel all the jobs for a user:

scancel -u <username>

To cancel one or more jobs by name:

scancel --name <myJobName>

It takes as an input a set of genomes represented as sequences of genes (or synteny blocks) and produces such sequences for ancestral genomes at the internal nodes of the phylogenetic tree.

The phylogenetic tree may be also specified completely or partially, in the latter case MGRA can reconstruct conserved ancestral regions (CARs) of the ancestral genome of interest.

Since version 2 MGRA supports gene insertion and deletions in addition to genome rearrangements and allows the input genomes to have different gene content.

It also can reconstruct most plausible phylogenetic tree based on the rearrangement characters.

Address of the bookmark: http://mgra.cblab.org/

Once a query gene has been entered, it is displayed in its genomic context in parallel to the genomic context of all its orthologous and paralogous copies in all the other sequenced metazoan genomes. Moreover, Genomicus stores and displays the predicted ancestral genome structure in all the ancestral species within the phylogenetic range of interest.

All the data on extant species displayed in this browser are from Ensembl.

Address of the bookmark: http://genomicus.biologie.ens.fr/genomicus-90.01/cgi-bin/search.pl

Address of the bookmark: https://github.com/reubwn/hgt

Address of the bookmark: https://sourceforge.net/projects/ksnp/files/