category: Sequence - DNA Sequencing and Assembly

programs:

• ABySS - de novo sequence assembler
• adaptercheck.py - Find potential read-through adapter contamination in sequencing reads
• blreads - Process and analyze DNA sequencing reads
• cutadapt - finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads
• dipspades - assembler for highly polymorphic diploid genomes
• fastq_pair - Remove non-paired reads from left or right read files
• fixfq.py - Divide a fastq file into two files, one with validated reads, and the other with reads that do not comply with the fastq format
• jellyfish - A fast k-mer counter
• magicblast - search for reads which match a custom sequence database
• pollux - DNA sequence read correction for all sequencing platforms
• samtools - Utilities for the Sequence Alignment/Map (SAM) format
• seqkit - FASTA/Q file manipulation
• SOAPdenovo2 - denovo genome assembler
• spades - Genome assembler
• trim_galore - sequenc quality trimming and adaptor removal
• Trimmomatic - Trim adaptors from sequencing reads
• truspades - assembler for short reads produced by Illumina TruSeq Long Read technology