| Bowtie |
1.1.0/2-2.2.3 |
An ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences |
Bowtie-<version> |
| Cd-hit |
4.6.1 |
A very widely used program for clustering and comparing protein or nucleotide sequences |
cd-hit-v<version> |
| Cutadapt |
1.4.2/1.8.1 |
Removes adapter sequences from high-throughput sequencing data |
Cutadapt/<version> |
| Exonerate |
2.2.0 |
A generic tool for pairwise sequence comparison |
Exonerate/<version> |
| Express |
1.5.1 |
eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences |
express-<version> |
| Fastqc |
1.5.1 |
Aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines |
Fastqc-<version> |
| GenomeAnalysisTK |
3.2-2 |
GATK tools for error modeling data compression and variant calling |
GenomeAnalysisTK-<version> |
| Maker |
2.31.8 |
MAKER is a portable and easily configurable genome annotation pipeline. |
Maker/<version> |
| Mothur |
1.33/1.35 |
Tool for analyzing 16S rRNA gene sequences. |
Mothur-<version> |
| Mummer |
3.23 |
A system for rapidly aligning entire genomes whether in complete or draft form. |
Mummer/<version> |
| Pandaseq |
2.8 |
A program to align Illumina reads optionally with PCR primers embedded in the sequence and reconstruct an overlapping sequence. |
Pandaseq/<version> |
| Qiime |
1.8 |
A program for comparison and analysis of microbial communities primarily based on high-throughput amplicon sequencing data. |
Qiime-<version> |
| Rsem |
1.2.16 |
A software package for estimating gene and isoform expression levels from RNA-Seq data. |
rsem-<version> |
| Samtools |
0.1.19 |
Provides various utilities for manipulating alignments in the SAM format including sorting merging indexing and generating alignments in a per-position format |
Samtools-<version> |
| SNAP |
0.1.19 |
A new sequence aligner that is 3-20x faster and just as accurate as existing tools like BWA-mem Bowtie2 and Novoalign |
SNAP/<version> |
| Trim-fastq |
1.2.2 |
A Fastq quality trimmer. |
Trim-fastq-<version> |
| Trinity |
r20140717 |
a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. |
Trinity |
