ソフトウェア

最新版のインストール済みソフトウェアを確認するには、module avail コマンド結果を参照ください

次世代シーケンサデータ解析用

hisat2 [1] HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA). 
stringtie [2] StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.

STAR [3] Spliced Transcripts Alignment to a Reference

salmon [4] Salmon is a tool for quantifying the expression of transcripts using RNA-seq data

samtools [5] SAM Tools provide various utilities for manipulating alignments in the SAM format

bamtools [6] Bamtools is a toolkit for analyzing and managing BAM files

BEDtools [7] Bedtools utilities are a tools for a wide-range of genomics analysis tasks

bwa [8] Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence

RSEM [9] RNA-Seq by Expectation-Maximization

soap [10] Short Oligonucleotide Analysis Package

bowtie [11] Bowtie is an ultrafast, memory-efficient short read aligner 
bowtie2 [12] Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
tophat [13] TopHat is a fast splice junction mapper for RNA-Seq reads
cufflinks [14] Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples

MACS2 [15] Model-based Analysis of ChIP-Seq on short reads sequencers such as Genome Analyzer (Illumina / Solexa)

GATK [16] The GATK is the industry standard for identifying SNPs and indels in germline DNA and RNAseq data.

次世代シーケンサデータ解析用：アセンブラー

Trinityrnaseq [17] Novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data

canu [18] Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION).

SPAdes [19] SPAdes – St. Petersburg genome assembler – is an assembly toolkit containing various assembly pipelines. 

velvet [20] Sequence assembler for very short reads

abyss [21] Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler

allpaths-lg [22]  The new short read genome assembler.

hifiasm [23]  Hifiasm is a fast haplotype-resolved de novo assembler for PacBio HiFi reads.

配列類似性検索

blast+ [24] Sequence Similarity Search

fasta [25] Sequence Similarity Search

blat [26] BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more

diamond [27] DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data.

MMseq2 [28] ultra fast and sensitive sequence search and clustering suite

vsearch [29]

ペアワイズアライメント

lastz [30] A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically

MUMmer [31] MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form.

マルチプルアライメント

clustalw  Multiple Sequence Alignment
clustalw2 [32] 
clustal Omega [33] Fast, accurate, scalable multiple sequence alignment for proteins

muscle [34] Multiple Sequence Alignment faster and more accurate than clustalw

mafft [35] MAFFT is a multiple sequence alignment program

t_coffee [36]  Multiple sequence alignment package

Gblocks  [37] Gblocks eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences

遺伝子情報取得

dbget　DBGET is an integrated database retrieval system for major biological databases

分子生物学用ソフトウェアパッケージ

EMBOSS [38] EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology

アセンブラー

CAP3 [39] Multiple Sequence Alignment
TGICL [40] Multiple Sequence Alignment (for huge data set)

Phred [41] The phred software reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base

Phrap　Phrap is a program for assembling shotgun DNA sequence data

consed　Assembly Editor

遺伝子領域予測

augustus [42] AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences

genemark [43] A family of gene prediction programs

genscan [44] Gene prediction

glimmer [45] Glimmer is a system for finding genes in microbial DNA

モチーフ検索

interproscan [46] A tool that combines different protein signature recognition methods into one resource

hmmer [47] Biosequence analysis using profile HMM

meme [48] Multiple Em for Motif Elicitation

系統樹解析

mrbayes [49] MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models

njplot [50] NJplot is a tree drawing program

paup [51] Tools for inferring and interpreting phylogenetic trees

phylip [52] A package of programs for inferring phylogenies (evolutionary trees)

phyml [53] PhyML is a phylogeny software based on the maximum-likelihood principle

tree-puzzle [54] Program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood

言語など

R [55] R is a free software environment for statistical computing and graphics.

python3

ruby