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- Circos
- IGV
- MaqView
- Mauve
- Affymetrix Integrated Genome Browser: easy to install genome browser. Download here
- SAMStat
De novo assembly
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- Convert ABI SOLiD data to fasta fastq
- General parser scripts - scripts for parsing and filtering of fasta, fastq files and output files from different mappers; base space, color space conversion scripts.
- Small rna analysis
- Generation of wig files from mapreads output
- Conversion of mapreads output to GFF, SAM, or BAM format - These utilities can be used to convert mapreads mapping output to base space format
- Generation of gene counts from results of mapping to genome - These scripts can be used to identify the reads that correspond to genes, after mapping to the genome.
- Get Tm (melting temperature), length, and %GC from a bunch of sequences
- Conversion of gene ID's from one form to another (i.e. NCBI to Ensembl & vice-versa)
- Quick tips on GO analysis
- Median polish to consolidate quantitations
- Make a quick venn diagram based on lists in 3 files
- Plot a read length histogram based on sequences in a fasta file
- Reverse complement for fasta files
- Tricks to preprocess SOLiD and 454 data
- Convert BLAST results to GFF
Software users group meetings
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