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• snippy error
• Metadata for assemblies deposited in NCBI
• Where can I get a fasta reference for all mob/rep genes?
• What is the best tool/wrokflow for a core SNP alignment?
• How do I download all genomes with specific ST type from ncbi
• PROKKA annotation problem - wrong reference?
• Problem setting blastdb in linux
• Where can I find a fasta for mitochondrial genes?
• HTSeq counts gives zero when I can see the reads in the BAM file
• bowtie2 --un vs --un-conc
• compare two groups of multiple bed files
• htseq-count without GTF?
• GFF3 transcript name
• R package or tool to draw peaks on chromosomes (like in UCSC)
• MSA program that allows collpase of identical reads
• Finding regulatory or structural elements
• Centrimo from the MEME-suit --neg option
• How can get overlap size in bedtools multi-intersect?
• How do I know if I have DNA contamination in RNA-seq data?
• Where can I find a list of mitochondrial tRNA locations?
• DB for small RNAs in plant genomes?
• high-throughput domain discovery
• Filtering noise out of SAM file using CIGAR
• Order of samtools mpileup - arbitrary or not?
• Can you get mpileup to report positions with coverage of 0?
• Lists of ncRNAS for cow, yeast
• IGV - is there a way to extract bulk information?
• BWA vs. bowtie
• Could not find or load main class net.sf.picard.sam.SortSam
• Database for MOUSE small RNAs?
• problem with BWA alignment
• fastq_quality_trimmer: Premature End-Of-File
• trim galore putfiles
• pileup format: what's the difference between upper and lower case?
• Recommendations for a good motif-finder, for short K-mers?
• bedtools shuffle vs. random
• Consensus secondary RNA stractures
• bowtie2 --un option problems
• cutadapt --cut option for paired-end reads?
• uneven paired end reads in bowtie
• How do I find an example of how to calculate FPKM with cufflinks?
• bcftools soft filters (-s)
• Bcftools magic string
• NGS tutorials (RNA)
• PE reads uneven after cutadapt
• determining read depth for every position in a sequence
• cutadapt -o versus >
• trim_galore finds a different adaptor than the one I expected...
• UCSC peak calling - weird results
• keeping trimmed edges
• Bam to WIG
• R1 and R2 in sequencing data
• How do I find unmapped reads in my sam file?
• is there a DB for illumina adaptors/contamination?
• where can I find more data about --outSAMattributes All?
• samtools mpileup giving QUAL of 0
• SNP call using bcftools
• Generate consensus from BAM file

After reading some more - should I map to reference with an aligner like BWA? or is there an assembly tool that uses a reference?