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Bioinformatic tools & resources

 

  • NGS tools

fastqc - a quality control tool for high throughput sequence data.

samtools - processing sequence alignments in SAM and BAM formats

HTSeq.py -

sickle - https://github.com/najoshi/sickle

seqtk - https://github.com/lh3/seqtk

sra-toolkit - The toolkit library provides the mechanism for inserting and search for information in the SRA database.

snpeff - It's a SNP effect predictor tool, it predicts the effect of genetic variations (SNPs, insertions and deletions) on genes.

bedtools - The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage.

bamtools - BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.

casava - http://support.illumina.com/sequencing/sequencing_software/casava/downloads.ilmn

fastx-toolkit - The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

picard-tools - Picard comprises Java-based command-line utilities that manipulate SAM files

 

  • Alignment

Bowtie - Bowtie is an ultrafast, memory-efficient short read aligner.

Bwa - Burrows-Wheeler Aligner

Soap - SOAP is a program for efficient gapped and ungapped alignment of short oligonucleotides onto reference sequences.

Blastall -

Blat -

ClustalW - global multiple nucleotide or peptide sequence alignment

ClustalX - Multiple alignment of nucleic acid and protein sequences (graphical interface)

t-coffee - Multiple Sequence Alignment

blastz - blastz alignment program

 

  • Assembly

Velvet  - Nucleic acid sequence assembler for very short reads

tigra-sv - http://gmt.genome.wustl.edu/tigra-sv/current/

CAP3 - CAP3 Assembly Program

Trinity (inchworm, cryalis, butterfly) - The inchworm RNA-Seq assembler, developed at the Broad Institute, employs the Kmer graph method

                                                                                to reconstruct (in many cases full-length) transcripts from Illumina RNA-Seq (preferrably strand-specific)

                                                                                reads. Inchworm is especially effective when used with strand-specific RNA-Seq data.

Soap-denovo -

Trans-Abyss -

 

  • Genome and variation analysis

cgatools - Tools developed by Complete genomics,  somatic, de novo variation calls, http://cgatools.sourceforge.net/docs/1.6.0/cgatools-command-line-

                      reference.html

samtools - processing sequence alignments in SAM and BAM formats

gatks -

Varscan2 - http://varscan.sourceforge.net/

snvmix2 - Detecting single nucleotide variants from next generation sequencing data

somaticsniper - http://gmt.genome.wustl.edu/somatic-sniper/current/

polyphen2 - http://genetics.bwh.harvard.edu/pph2/

provean - http://provean.jcvi.org/index.php

JoinSNVMix - http://compbio.bccrc.ca/software/jointsnvmix/

Breakdancer - BreakDancerMax predicts five types of structural variants:

CREST - http://www.stjuderesearch.org/site/lab/zhang

tea - http://compbio.med.harvard.edu/Tea/

meerkat - http://compbio.med.harvard.edu/Meerkat/

GISTIC2.0 - http://www.broadinstitute.org/cancer/pub/GISTIC2/

 

  • RNA-seq analysis

Tophat - TopHat is a fast splice junction mapper for RNA-Seq reads.

Cufflinks - Cufflinks assembles transcripts and estimates their abundances in RNA-Seq samples.

Tophat-fusion

edgeR -  Empirical analysis of digital gene expression  data in R

Cuffdiff

 

 

  • RNA analysis

RNAfold

mfold

Sylamer - Motif enrichment analysis with fold changes of RNAs (http://www.ebi.ac.uk/research/enright/software)

mirdeep - The miRDeep package was developed to discover active known or novel miRNAs from deep sequencing data (Solexa/Illumina, 454, ...).

 

  • lncRNAs

Cpc - http://cpc.cbi.pku.edu.cn/download/

RNACode - RNAcode predicts protein coding regions in a a set of homologous nucleotide sequences.

phyloCSF

RRS

 

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