Must-have Tools for a Bioinformatician

Must-have Tools for a Bioinformatician


A friend of mine got so overwhelmed after receiving seven large hiSEQ libraries (to be assembled in a week) that she deleted everything from her hard-drive. Trying to show the bright side of things, I told her that this would be a great opportunity to clean all clutter from her server (done :) ) and install only the top quality programs that she will use again and again. Can you suggest some programs that you use very frequently? Here is the list I came up with. Please feel free to add.

A. Sequence Search

Sequence search is one of the tasks bioinformaticians do day in and out. The purpose of those searches vary. Let me list a few here.

(i) You have a protein sequence and you want to find out whether it matches any other protein that people have already studied.

(ii) You have a large library (100M) of Illumina reads from human genome and you like to match them against the reference genome to find SNPs.

(iii) You have a long EST from an Arabidopsis sample and you want to find its coordinates on the Arabidopsis genome.

(iv) You have a peptide sequence from mouse, but do not know its gene sequence. You like to find out the gene sequence by searching the peptide against the mouse genome.

You can see that those four examples need different capabilities from the search program and your computer. For example, the second one can assume that the matches will be near exact, and use that information to speed up the search process. On the other hand, the first example cannot make that compromise, but speed may not be an issue, when you are searching for only one or few proteins instead of 100M.

A bioinformatician needs to have many types of search programs to fit various purposes. Here is the core set I recommend -

NCBI BLAST

Purpose

This is the all-purpose sequence homlogy search program that every biologist is familiar with. One can use BLAST to search nucleotide sequence against protein database, nucleotide against nucleotide database, peptide against nucleotide database or peptide against protein database.

Download from

NCBI ftp site

Installation

Installation is easy. Download the right executable for your type of computer and nothing else needs to be done other than setting path.

Common commands

preparing database: formatdb -i [FASTA reference dbname] -p F -o T

nucl against nucl: blastall -i [FASTA seq] -d [ref dbname] -p blastn -e 1e-10 -o [output]

nucl against nucl: blastall -i [FASTA seq] -d [ref dbname] -p blastp -e 1e-10 -o [output]

nucl against nucl: blastall -i [FASTA seq] -d [ref dbname] -p blastn -e 1e-10 -o [output]

nucl against nucl: blastall -i [FASTA seq] -d [ref dbname] -p blastn -e 1e-10 -o [output]

Online references

NCBI

Weakness

BLAST is too slow for searching sequences that map exactly on a genome, and especially for mapping large libraries of short reads on a reference genome.

Alternative - HMMER (claims to be far more accurate than BLAST or FASTA for protein homology search), FASTA. Also note that many variations of BLAST exist, such as megaBLAST, WU-BLAST, etc.

BLAT

Purpose

BLAT is used for mapping a long sequence that matches a genome near exactly.

Download from

UCSC ftp site

Installation

Installation is easy. Download the right executable for your type of computer and nothing else needs to be done other than setting path.

Common command

blat [database] [query] [output]

Online references

UCSC

Weakness

BLAT is best for mapping ESTs on a reference genome, and it reports all splice junctions properly. Don’t use it for any other purpose.

Alternative - exonerate from EBI.

Bowtie/Tophat/Cufflink

Purpose

Quick mapping of large number of short read sequences on a reference genome, and constructing gene sequences.

Download from

Bowtie website at sourceforge

Installation

Installation is easy. Download the right executable for your type of computer and nothing else needs to be done other than setting path.

Common command

building index: bowtie-build [reference] [index]

unpaired reads: bowtie [index] [read file] [output]

paired reads: bowtie [index] -1 [left read] -2 [right read] [output]

Online references

Tutorial

Manual

Weakness

Primarily for short reads. Requires near perfect match.

Alternatives - BWA, MAQ, Shrimp.

B. Multiple Sequence Alignment

Clustal (clustalw2)

Purpose

Clustal is perfect for aligning large number of similar sequences (nucleotide or protein) and find their common segments.

Download from

EBI ftp site

Installation

Installation is easy. Download the right executable for your type of computer and nothing else needs to be done other than setting path.

Common command

clustalw2 [FASTA sequence]

Online references

Clustal manual

Weakness

Performs poorly, if any sequence has large N block.

Alternative - BLAST.

C. SNP Analysis

Samtools

Purpose

Samtools is the most efficient program to store and access large number of short read alignments. SAM format has almost become a standard now.

Download from

Sourceforge site

Installation

Installation is easy. Download the right executable for your type of computer and nothing else needs to be done other than setting path.

Common command

Check the synopsis section at the top of this page.

Online references

samtools manual

samtools FAQ

Weakness

Alternative - SOAPsnp.

D. Assembly

CAP3

Purpose

A very versatile assembly program, when the number of reads is not very high.

Download from

Author’s site

Installation

Installation is easy. Download the right executable for your type of computer. That is all.

Common command

cap3 [fasta file]

Online references

Documentation

Weakness

This is an overlap and extend type of program. De Bruijn assemblers are better for large library of short reads.

Newbler

Among all programs listed here, Newbler is the only one I never used. However, everyone using 454 data recommends it. The software comes from Roche and here is how you get it in various countries of the world. Source code is proprietary and it is not a de Bruijn assembler.

SOAPdenovo

Purpose

One of the best de Bruijn assemblers around, both in terms of performance and memory requirement.

Download from

BGI website

Installation

Installation is easy. You can download the executable from their website.

Common command

Check here.

Online references

BGI website for SOAPdenovo

Weakness

Source code unavailable.

Velvet

Purpose

De Bruijn assembler for genomic data. Works great for color space.

Download from

EBI website

Installation

‘make’ or ‘make color’

Common command

velveth out 21 -shortPaired reads.fa

velvetg out

Online references

Manual. Also Velvet mailing list is very active.

Weakness

Requires large RAM. Also, it is not good for transcriptome data, unless you also use Oases.

Oases

Purpose

De Bruijn assembler for transcriptome that works on Velvet output.

Download from

Oases website at EBI

Installation

make ‘VELVET_DIR=/path/to/velvet’ [check manual for color space installation]

Common command

velveth out 21 -shortPaired reads.fa

velvetg out -read_trkg yes

oases out -ins_length 200

Online references -

UCSC. Also, Oases mailing list is very active.

Weakness

Needs even more RAM than Velvet.

Trinity

Purpose

De Bruijn assembler for transcriptome.

Download from

sourceforge website for trinity

Installation

You need Java in your machine. C/C++ part needs to be compiled with ‘make’. Java part is already compiled.

Common command

Trinity.sh –seqType fq –left l.fq –right r.fq –output outdir

Online references

Trinity manual

Weakness

Inchworm step is very slow.

Alternatives - Abyss (parallel assembler for MPI machines), Contrail (parallel assembler for hadoop), Euler, ALLpaths- LG.

E. Protein Function Analysis

BLAST against NCBI NR

Interpro scan

F. Statistical Analysis

R

G. Microarray data

Bioconductor module in R

limma package

Common commands: lmFit, eBayes, topTable

H. Sharing and Visualization

IGV

I. Colorspace

ABI Color space library

We covered all of four above topics in various posts here.

J. Bonus tools

ssaha2

hmmer

Mummer

Stampy

repeatmasker

Hadoop

-———————-

Here are few places I go to to find information on latest software packages -

i) Seqanswers Wiki

ii) Bioinformatics tools at EBI

iii) List of all resources at NCBI, and sub list of bioinformatic tools.

iv) Computational tools at BROAD institute

v) Software tools from UCSC.


Written by M. //

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