Search:

sci-biology/prinseq-lite

Describe, trim, reformat and convert to or form FASTA/FASTQ files

sci-biology/rnaplex

RNA-RNA interaction search

sci-biology/skewer-bin

Adaptor and MID removal / trimming tool

sci-biology/smalt-bin

Pairwise sequence alignment mapping DNA reads onto genomic reference

sci-biology/smalt

DNA read mapper using k

sci-biology/spm

Analysis of brain imaging data sequences for Octave or Matlab

sci-biology/subread

NGS suite for analysis of mapped reads, summary of exon/intron/gene counts

sci-biology/tagdust

Trim multimers of various primers/adapter from Illumina datasets

sci-biology/wgs_tools

Scripts for ncbi-tools++ and SRA postprocessing using taxonomy

sci-biology/MaSuRCA

de Bruijn and OLC assembler for Sanger, Roche 454, Illumina, Pacbio, Nanopore

sci-biology/libBigWig

C library for handling bigWig files (functionally replacing Jim Kent's lib)

sci-biology/seqtools

Display alignments and GFF files, matrix dot plots (blixem, dotter, belvu)

sci-biology/gffcompare

Compare, classify, merge, track, annotate GFF files

sci-biology/stringtie

Transcriptome assembler and RNA-Seq analysis on BAM files aka cufflinks

sci-biology/samri_bindata

ParaVision Mouse, Rat, and Lemur Testing Data for SAMRI

sci-biology/seqtk

Manipulate FASTA and FASTQ files

sci-biology/samri_bidsdata

BIDS-formatted example mouse brain data for SAMRI

sci-biology/zmap

A desktop genome browser using GFF inputs

sci-biology/ParaAT

Create multiple protein-coding DNA alignments and back-Translation

sci-biology/CAT

Codon usage bias (composition) and its statistical significance

sci-biology/lemur-brain-atlas

MRI Brain Template and Atlas of the Mouse Lemur

sci-biology/portrait

Ab initio ncRNA prediction

sci-biology/VelvetOptimiser

Optimise Velvet sequence assembler

sci-biology/ABI-connectivity-data

Connectivity data from the Allen Mouse Brain data portal

sci-biology/drlfom_bidsdata

BIDS data files released with the DRLFOM publication

sci-biology/irsabi_bidsdata

BIDS data files released with the IRSABI publication

sci-biology/opfvta_bidsdata

BIDS data files released with the OPFVTA publication

sci-biology/ABI-expression-data

Gene expression data form the Allen Mouse Brain data portal

sci-biology/ONTO-PERL

Manipulates OBO- and OWL-formatted ontologies (like the Gene Ontology)

sci-biology/TransDecoder

Extract ORF/CDS regions from FASTA sequences

sci-biology/bismark

Map bisulfite converted sequence reads and cytosine methylation states

sci-biology/brat

Bisulfite-treated Reads Analysis Tool (short read mapper)

sci-biology/brat_nova

Bisulfite-aware short read mapper, FM-index, accepts 1 InDel/read, local align

sci-biology/brat_bw

Bisulfite-aware short read mapper, FM-index, no InDel support

sci-biology/edena

De novo short read OLC assembler (overlap-layout-consensus)

sci-biology/erpin

Easy RNA Profile IdentificatioN, an RNA motif search program

sci-biology/fsl

Analysis of functional, structural, and diffusion MRI brain imaging data

sci-biology/gffread

GFF/GTF utility providing format conversions, filter/extract regions from FASTA

sci-biology/hexamer

Predict CDS using 6mers without deriving information from base composition

sci-biology/karect

Error-correct mismatches and InDels of raw reads incl. paired-end

sci-biology/mip-scaffolder

Scaffold contigs using ABI Solid or Illumina mate pair info

sci-biology/mreps

Identification of serial/tandem repeats in DNA sequences

sci-biology/msautil

Reformat/edit FASTA files and compute simple statistics (N50, quartiles, mode)

sci-biology/pairagon

HMM-based cDNA to genome aligner

sci-biology/psx

parallel multi-FASTA file processing tool from TIGR Gene Indices project tools

sci-biology/quicktree

Rapid reconstruction of phylogenies by the Neighbor-Joining method

sci-biology/sff_dump

Convert Roche SFF files to FASTA file format

sci-biology/ssaha2-bin

SSAHA2: Sequence Search and Alignment by Hashing Algorithm

sci-biology/verifyBamID

Verify sample identity/mix and genotype concordance

sci-biology/zmsort

Merge-sort utility for compressed alignment files, with multi-file output