- Evaluating your raw sequencing data
- counting sequences: fastq and fastq.gz
- quality assurance: FASTQC and samstats
- Determining the quality and complexity of next-generation sequencing data without a reference genome
- trimming and de-multiplexing: Trimmomatic, Fastx_toolkit, fastx_trimmer, cutadapt, trim_galore, condetri, flexor (https://github.com/seqan/flexbar)
- genotype detection, reference selection
- alignment: bowtie2, bwa, tanoti
- post alignment stats:
- weeSAM - python script for various coverage statistics (legacy versions in perl)
- SamRemoveIndels - awk script to remove reads with indels from a SAM file
- UniqSamPE - awk script to remove paired-end fragments that start and end at the exact same position
- post alignment analysis: haplotype window, remove primer reads, detecting chimeras
- consensus calling
- variant calling (link to ValVs)