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| SOLiD™ System SRF Conversion Tool | srf | Applied Biosystems SOLiD™ System Sequence Read Format Conversion Tool | ||||||||
| SOLiD™ System Small RNA Analysis Tool | rna2map | Applied Biosystems SOLiD™ System Human Small RNA Analysis Pipeline Tool | ||||||||
| SOLiD™ System Human (Yoruban) data | yoruban | Applied Biosystems SOLiD™ System Human (Yoruban) variation data | ||||||||
| SOLiD™ System Human Small RNA Data | srna | Applied Biosystems SOLiD™ System Human Small RNA Data Set | ||||||||
| SOLiD™ System GFF Conversion Tool | matogff | Applied Biosystems SOLiD™ System General Feature Format Conversion Tool | ||||||||
| SOLiD™ System E. Coli DH10B Fragment | dh10bfrag | Applied Biosystems SOLiD™ System E.Coli DH10B Fragment Data | ||||||||
| SOLiD™ System E. Coli DH10B 2X50 Data | ecoli2x50 | This data set was sequenced using the SOLiD™ System. It consists of a sequence run from a 2X50 mate-pair library. (and represents 293 panels of data or 1/8 of a slide totaling 58 million reads. It is approximately a 200X coverage of the E. Coli DH10B genome.) | ||||||||
| SOLiD™ System de Novo Accessory Tools | denovo | SOLiD™ System de Novo Accessory Tools | ||||||||
| SOLiD™ System Color Space Mapping Tool | mapreads | Applied Biosystems SOLiD™ System Color Space Alignment Tool | ||||||||
| SOLiD™ System Analysis Pipeline Tool | corona | Applied Biosystems SOLiD™ System Whole Genome Analysis Pipeline Tool | ||||||||
| SOLiD™ System Alignment Browser | sab | Applied Biosystems SOLiD™ System SOLiD™ Alignment Browser | ||||||||
| SOLiD™ SAGE™ Analysis Software | solid-sage | SOLiD™ SAGE™ Analysis Software is a tool for taking the raw sequence data files from SOLiD™ SAGE™ reads and matching them to known sequences in your reference database of choice. It is designed for use with the SOLiD™ SAGE™ kit, which generates libraries of 27-bp tags for all transcripts in a cell. | ||||||||
| SOLiD BaseQV Tool | sam | Tool for the conversion of SOLID output files to base data with associated quality values | ||||||||
| SOCS | socs | Color space alignment tool | ||||||||
| SHRiMP -- SHort Read Mapping Package | shrimp | SHRiMP is a tool for mapping short read data in color-space or letter-space | ||||||||
| SAET | saet | The SOLiD™ Accuracy Enhancer Tool (SAET) uses raw data generated by SOLiD™ Analyzer to correct miscalls within reads prior to mapping or contig assembly. | ||||||||
| RNA-MATE | rnamate | A whole-transcriptome recursive mapping strategy for RNAseq data. | ||||||||
| PerM | perm | PerM is an ultra-fast and sensitive SOLiD reads mapping tool. It maps reads in csfasta (w/wo qual), fasta or fastq format to the genome or transcriptoms in fasta. The output could be the SAM format. PerM can be full sensitive to four mismatches and highly sensitive to more mismatches. | ||||||||
| Instructions of Account Use | account | Instructions of Account Use | ||||||||
| GejiGeji: a depth visualize tool. | gejigeji | GejiGeji is a Java software to create and view some images for depth or coverage information from some 'fwd_rev_coverage.txt' files. | ||||||||
| Galaxy | galaxy | Galaxy is a web-based framework that integrates data sources and tools, making analysis simple and reproducible. | ||||||||
| denovo assembly tools | denovotools | Improved denovo assembly preprocessor and postprocessor | ||||||||
| CNV-seq | cnvseq | CNV-seq is an implementation of a new method to detect copy number variation using high-throughput sequencing, published in BMC Bioinformatics 2009, 10:80. More details can be found from the CNV-seq home page and the original paper. | ||||||||
| BFAST Blatlike Fast Accurate Search Tool | bfast | BFAST facilitates the fast and accurate mapping of short reads to reference sequences. | ||||||||
| ADiR: Assembler for Di-base Reads | adir | An assembler for colorspace reads that makes use of color transition properties in resolving overlap and consensus. | ||||||||
| AB WT Analysis Pipeline | transcriptome | Applied Biosystems AB Whole Transcriptome Analysis Pipeline will allow you to map transcript reads to a reference genome, count both exon and gene tags, and export data in a format that can be viewed in the UCSC browser. | ||||||||
| AB Small Indel Tool | indel | Applied Biosystems AB Small Indel Tool to identify small INDELs in data generated by the SOLID system | ||||||||
| AB Large InDel Tool | large_indel | AB Large Indel Tool | ||||||||
| AB Inversion Tool | inversion | Applied Biosystems Inversion Tool to identify inversions in data generated by the SOLID system | ||||||||
| AB diBayes SNP Tool | dibayes | diBayes | ||||||||
| AB CNV Tool | cnv | AB CNV Tool | ||||||||
| AB Chip-Seq Accessory Tools | chipseq | AB Chip-Seq Accessory Tools | ||||||||
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