Revision as of 16:06, 31 March 2013

Notes on software of interest:

Misc

Software lists:

http://en.bio-soft.net/dna.html

Sequencing/genome assembly

SeqAnswers - Software packages for next gen sequence analysis: http://seqanswers.com/forums/showthread.php?t=43

SAM Tools:

http://samtools.sourceforge.net/

http://samtools.sourceforge.net/samtools.shtml

Bowtie:

http://seqanswers.com/forums/showthread.php?t=706

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome: http://genomebiology.com/2009/10/3/R25

http://bowtie-bio.sourceforge.net/index.shtml

Bowtie vs. BWA: http://seqanswers.com/forums/showthread.php?t=15200

Short Oligonucleotide Alignment Package (SOAP):

http://soap.genomics.org.cn/

Description from SeqAnswers: "A program for efficient gapped and ungapped alignment of short oligonucleotides onto reference sequences. The updated version uses a BWT. Can call SNPs and INDELs. Author is Ruiqiang Li at the Beijing Genomics Institute."

The initial version, SOAP v1, is a program for gapped and ungapped alignment of short reads to a reference sequence. SOAP has been expanded to a package with several new programs, including:

SOAPdenovo, "a short read de novo assembly tool, is a package for assembling short oligonucleotide into contigs and scaffolds."
SOAPaligner/soap2
SOAPsnp
SOAPindel

Burrows-Wheeler Aligner (BWA):

" a software package for mapping low-divergent sequences against a large reference genome"/ http://bio-bwa.sourceforge.net/)

Three algorithms:

BWA-backtrack (Reads up to 100 nt)
BWA-SW (For longer reads: 70 nt - 1Mb)
BWA-MEM (For longer reads: 70 nt - 1 Mb. Faster and more accurate than BWA-SW)

BWA is an aligner only, and does not call SNPs or other variations.

Article: Fast and accurate short read alignment with Burrows-Wheeler transform: http://www.ncbi.nlm.nih.gov/pubmed/19451168

Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM: http://arxiv.org/abs/1303.3997

Assembly By Short Sequences (ABySS):

http://www.bcgsc.ca/platform/bioinfo/software/abyss

"A de novo, parallel, paired-end sequence assembler."

Euler-SR:

https://ngslib.genome.tugraz.at/node/64

Genome/sequence data analysis

Sequence Assembly Manager (SAM): http://www.bcgsc.ca/platform/bioinfo/software/sam

Description: "SAM is a Whole Genome Assembly (WGA) Management and Visualization Tool. It provides a generic platform for manipulating, analyzing and viewing WGA data, regardless of input type."

Integrative Genomics Viwer: http://www.broadinstitute.org/software/igv/home

Open Genomics Engine: http://www.opengenomicsengine.org/learn/

DNAsp: http://bioinformatics.oxfordjournals.org/content/25/11/1451

http://www.jalview.org/