User:Jarle Pahr/Software
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):
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
Rapid Identification of Non-human Sequences (RINS): http://khavarilab.stanford.edu/resources.html
Misc
FASTA software package: http://fasta.bioch.virginia.edu/fasta_www2/fasta_list2.shtml